******take a break***********
refolder,unzip and FastQC codes:
********(checkout bowtie condor file)*********
cat Sample_20994Index__1_42AB_UASG_1/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20994Index__1_42AB_UASG_1_Sample_20994Index__1_42AB_UASG_1*fastq & 
cat Sample_20995Index__2_42AB_UASG_2/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20995Index__2_42AB_UASG_2_Sample_20995Index__2_42AB_UASG_2*fastq &
cat Sample_20996Index__3_66A_UASG_1/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20996Index__3_66A_UASG_1_Sample_20996Index__3_66A_UASG_1*fastq &
cat Sample_20997Index__4_66A_UASG_2/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20997Index__4_66A_UASG_2_Sample_20997Index__4_66A_UASG_2*fastq &
cat Sample_20998Index__5_42AB_UBIG_1/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20998Index__5_42AB_UBIG_1_Sample_20998Index__5_42AB_UBIG_1*fastq &
cat Sample_20999Index__6_42AB_UBIG_2/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_20999Index__6_42AB_UBIG_2_Sample_20999Index__6_42AB_UBIG_2*fastq &
cat Sample_21000Index__7_66A_UBIG_1/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21000Index__7_66A_UBIG_1_Sample_21000Index__7_66A_UBIG_1*fastq &
cat Sample_21001Index__8_66A_UBIG_2/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_21001Index__8_66A_UBIG_2_Sample_21001Index__8_66A_UBIG_2*fastq &
cat Sample_23572Index__1_190_het_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23572Index__1_190_het_piRNA_1st_Sample_23572Index__1_190_het_piRNA_1st*fastq &
cat Sample_23573Index__2_190_het_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23573Index__2_190_het_piRNA_2nd_Sample_23573Index__2_190_het_piRNA_2nd*fastq &
cat Sample_23574Index__3_190_558_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23574Index__3_190_558_piRNA_1st_Sample_23574Index__3_190_558_piRNA_1st*fastq &
cat Sample_23575Index__4_190_558_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23575Index__4_190_558_piRNA_2nd_Sample_23575Index__4_190_558_piRNA_2nd*fastq &
cat Sample_23576Index__5_32833-1-7M_het_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23576Index__5_32833-1-7M_het_piRNA_1st_Sample_23576Index__5_32833-1-7M_het_piRNA_1st*fastq &
cat Sample_23577Index__6_32833-1-7M_het_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23577Index__6_32833-1-7M_het_piRNA_2nd_Sample_23577Index__6_32833-1-7M_het_piRNA_2nd*fastq &
cat Sample_23578Index__7_32833-1-7M_558_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23578Index__7_32833-1-7M_558_piRNA_1st_Sample_23578Index__7_32833-1-7M_558_piRNA_1st*fastq &
cat Sample_23579Index__8_32833-1-7M_558_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_23579Index__8_32833-1-7M_558_piRNA_2nd_Sample_23579Index__8_32833-1-7M_558_piRNA_2nd*fastq &
cat Sample_311_20A_hom_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_1st_Sample_311_20A_hom_piRNA_1st*fastq &
cat Sample_311_20A_hom_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_hom_piRNA_2nd_Sample_311_20A_hom_piRNA_2nd*fastq &
cat Sample_311_20A_X_Zuc_KD_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_1st_Sample_311_20A_X_Zuc_KD_1st*fastq &
cat Sample_311_20A_X_Zuc_KD_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_20A_X_Zuc_KD_2nd_Sample_311_20A_X_Zuc_KD_2nd*fastq &
cat Sample_311_male_FM7c_311_female_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_1st_Sample_311_male_FM7c_311_female_1st*fastq &
cat Sample_311_male_FM7c_311_female_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_311_female_2nd_Sample_311_male_FM7c_311_female_2nd*fastq &
cat Sample_311_male_FM7c_G0_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_1st_Sample_311_male_FM7c_G0_1st*fastq &
cat Sample_311_male_FM7c_G0_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G0_2nd_Sample_311_male_FM7c_G0_2nd*fastq &
cat Sample_311_male_FM7c_G3_active_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_1st_Sample_311_male_FM7c_G3_active_1st*fastq &
cat Sample_311_male_FM7c_G3_active_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_active_2nd_Sample_311_male_FM7c_G3_active_2nd*fastq &
cat Sample_311_male_FM7c_G3_intermingled_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_1st_Sample_311_male_FM7c_G3_intermingled_1st*fastq &
cat Sample_311_male_FM7c_G3_intermingled_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_intermingled_2nd_Sample_311_male_FM7c_G3_intermingled_2nd*fastq &
cat Sample_311_male_FM7c_G3_silence_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_1st_Sample_311_male_FM7c_G3_silence_1st*fastq &
cat Sample_311_male_FM7c_G3_silence_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G3_silence_2nd_Sample_311_male_FM7c_G3_silence_2nd*fastq &
cat Sample_311_male_FM7c_G8_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_1st_Sample_311_male_FM7c_G8_1st*fastq &
cat Sample_311_male_FM7c_G8_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_male_FM7c_G8_2nd_Sample_311_male_FM7c_G8_2nd*fastq &
cat Sample_311_maternal_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_1st_Sample_311_maternal_piRNA_1st*fastq &
cat Sample_311_maternal_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_2nd_Sample_311_maternal_piRNA_2nd*fastq &
cat Sample_311_maternal_piRNA_Rhi_KD_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_1st_Sample_311_maternal_piRNA_Rhi_KD_1st*fastq &
cat Sample_311_maternal_piRNA_Rhi_KD_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_Rhi_KD_2nd_Sample_311_maternal_piRNA_Rhi_KD_2nd*fastq &
cat Sample_311_maternal_piRNA_White_KD_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_1st_Sample_311_maternal_piRNA_White_KD_1st*fastq &
cat Sample_311_maternal_piRNA_White_KD_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_maternal_piRNA_White_KD_2nd_Sample_311_maternal_piRNA_White_KD_2nd*fastq &
cat Sample_311_Paternal_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_1st_Sample_311_Paternal_piRNA_1st*fastq &
cat Sample_311_Paternal_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_Paternal_piRNA_2nd_Sample_311_Paternal_piRNA_2nd*fastq &
cat Sample_311_piRNA_maternal_to_313_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_1st_Sample_311_piRNA_maternal_to_313_1st*fastq &
cat Sample_311_piRNA_maternal_to_313_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_313_2nd_Sample_311_piRNA_maternal_to_313_2nd*fastq &
cat Sample_311_piRNA_maternal_to_314_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_1st_Sample_311_piRNA_maternal_to_314_1st*fastq &
cat Sample_311_piRNA_maternal_to_314_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_314_2nd_Sample_311_piRNA_maternal_to_314_2nd*fastq &
cat Sample_311_piRNA_maternal_to_333_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_1st_Sample_311_piRNA_maternal_to_333_1st*fastq &
cat Sample_311_piRNA_maternal_to_333_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_311_piRNA_maternal_to_333_2nd_Sample_311_piRNA_maternal_to_333_2nd*fastq &
cat Sample_313_20A-_hom_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_1st_Sample_313_20A-_hom_piRNA_1st*fastq &
cat Sample_313_20A-_hom_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_313_20A-_hom_piRNA_2nd_Sample_313_20A-_hom_piRNA_2nd*fastq &
cat Sample_314_20A-_hom_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_1st_Sample_314_20A-_hom_piRNA_1st*fastq &
cat Sample_314_20A-_hom_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_314_20A-_hom_piRNA_2nd_Sample_314_20A-_hom_piRNA_2nd*fastq &
cat Sample_32043-1-1F_20A_UBIGasG_-_hom_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_1st_Sample_32043-1-1F_20A_UBIGasG_-_hom_1st*fastq &
cat Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd_Sample_32043-1-1F_20A_UBIGasG_-_hom_2nd*fastq &
cat Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_1st*fastq &
cat Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd_Sample_32043-1-5F_20A_UBIGasG_Plus_hom_2nd*fastq &
cat Sample_333_piRNA_maternal_to_313_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_1st_Sample_333_piRNA_maternal_to_313_1st*fastq &
cat Sample_333_piRNA_maternal_to_313_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_313_2nd_Sample_333_piRNA_maternal_to_313_2nd*fastq &
cat Sample_333_piRNA_maternal_to_314_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_1st_Sample_333_piRNA_maternal_to_314_1st*fastq &
cat Sample_333_piRNA_maternal_to_314_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_333_piRNA_maternal_to_314_2nd_Sample_333_piRNA_maternal_to_314_2nd*fastq &
cat Sample_447_42A15-_Rhi_KD_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_1st_Sample_447_42A15-_Rhi_KD_piRNA_1st*fastq &
cat Sample_447_42A15-_Rhi_KD_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Rhi_KD_piRNA_2nd_Sample_447_42A15-_Rhi_KD_piRNA_2nd*fastq &
cat Sample_447_42A15-_Zuc_KD_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_1st_Sample_447_42A15-_Zuc_KD_piRNA_1st*fastq &
cat Sample_447_42A15-_Zuc_KD_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_447_42A15-_Zuc_KD_piRNA_2nd_Sample_447_42A15-_Zuc_KD_piRNA_2nd*fastq &
cat Sample_477_42A15-_control_het_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_1st_Sample_477_42A15-_control_het_1st*fastq &
cat Sample_477_42A15-_control_het_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_477_42A15-_control_het_2nd_Sample_477_42A15-_control_het_2nd*fastq &
cat Sample_654_TM3_UBIGasG_66A6_male311_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_1st_Sample_654_TM3_UBIGasG_66A6_male311_1st*fastq &
cat Sample_654_TM3_UBIGasG_66A6_male311_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_TM3_UBIGasG_66A6_male311_2nd_Sample_654_TM3_UBIGasG_66A6_male311_2nd*fastq &
cat Sample_654_UBIGasG_66A6plus_hom_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_1st_Sample_654_UBIGasG_66A6plus_hom_1st*fastq &
cat Sample_654_UBIGasG_66A6plus_hom_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_hom_2nd_Sample_654_UBIGasG_66A6plus_hom_2nd*fastq &
cat Sample_654_UBIGasG_66A6plus_male311_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_1st_Sample_654_UBIGasG_66A6plus_male311_1st*fastq &
cat Sample_654_UBIGasG_66A6plus_male311_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_654_UBIGasG_66A6plus_male311_2nd_Sample_654_UBIGasG_66A6plus_male311_2nd*fastq &
cat Sample_Female630_1-1F_UBIGasG_minus_male311_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_1st_Sample_Female630_1-1F_UBIGasG_minus_male311_1st*fastq &
cat Sample_Female630_1-1F_UBIGasG_minus_male311_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female630_1-1F_UBIGasG_minus_male311_2nd_Sample_Female630_1-1F_UBIGasG_minus_male311_2nd*fastq &
cat Sample_Female632_1-5F_UBIGasG_plus_male311_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_1st_Sample_Female632_1-5F_UBIGasG_plus_male311_1st*fastq &
cat Sample_Female632_1-5F_UBIGasG_plus_male311_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Female632_1-5F_UBIGasG_plus_male311_2nd_Sample_Female632_1-5F_UBIGasG_plus_male311_2nd*fastq &
cat Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_1st*fastq &
cat Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd_Sample_FemaleFM7i_1-1F_UBIGasG_minus_male_311_2nd*fastq &
cat Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_1st*fastq &
cat Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd_Sample_FemaleFM7i_1-5F_UBIGasG_plus_male_311_2nd*fastq &
cat Sample_index10_42AB_start_plus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index10_42AB_start_plus_piRNA_2nd_Sample_index10_42AB_start_plus_piRNA_2nd*fastq &
cat Sample_index11_42A15_minus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index11_42A15_minus_piRNA_1st_Sample_index11_42A15_minus_piRNA_1st*fastq &
cat Sample_index12_42A15_minus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index12_42A15_minus_piRNA_2nd_Sample_index12_42A15_minus_piRNA_2nd*fastq &
cat Sample_index13_42A15_plus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index13_42A15_plus_piRNA_1st_Sample_index13_42A15_plus_piRNA_1st*fastq &
cat Sample_index1_42A18_minus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index1_42A18_minus_piRNA_1st_Sample_index1_42A18_minus_piRNA_1st*fastq &
cat Sample_index14_42A15_plus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index14_42A15_plus_piRNA_2nd_Sample_index14_42A15_plus_piRNA_2nd*fastq &
cat Sample_index15_20A_minus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index15_20A_minus_piRNA_1st_Sample_index15_20A_minus_piRNA_1st*fastq &
cat Sample_index16_20A_minus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index16_20A_minus_piRNA_2nd_Sample_index16_20A_minus_piRNA_2nd*fastq &
cat Sample_index18_ActinG_plus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index18_ActinG_plus_piRNA_1st_Sample_index18_ActinG_plus_piRNA_1st*fastq &
cat Sample_index19_ActinG_plus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index19_ActinG_plus_piRNA_2nd_Sample_index19_ActinG_plus_piRNA_2nd*fastq &
cat Sample_Index20_20A_minus_piRNA_1/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index20_20A_minus_piRNA_1_Sample_Index20_20A_minus_piRNA_1*fastq &
cat Sample_index20_Moon_wt_190_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index20_Moon_wt_190_piRNA_1st_Sample_index20_Moon_wt_190_piRNA_1st*fastq &
cat Sample_Index21_20A_minus_piRNA_2/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_Index21_20A_minus_piRNA_2_Sample_Index21_20A_minus_piRNA_2*fastq &
cat Sample_index21_Moon_wt_190_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index21_Moon_wt_190_piRNA_2nd_Sample_index21_Moon_wt_190_piRNA_2nd*fastq &
cat Sample_index22_Moon_mutant_190_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index22_Moon_mutant_190_piRNA_1st_Sample_index22_Moon_mutant_190_piRNA_1st*fastq &
cat Sample_index23_Moon_mutant_190_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index23_Moon_mutant_190_piRNA_2nd_Sample_index23_Moon_mutant_190_piRNA_2nd*fastq &
cat Sample_index2_42A18_minus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index2_42A18_minus_piRNA_2nd_Sample_index2_42A18_minus_piRNA_2nd*fastq &
cat Sample_index3_Pld_intron_plus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index3_Pld_intron_plus_piRNA_1st_Sample_index3_Pld_intron_plus_piRNA_1st*fastq &
cat Sample_index4_Pld_intron_plus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index4_Pld_intron_plus_piRNA_2nd_Sample_index4_Pld_intron_plus_piRNA_2nd*fastq &
cat Sample_index5_Pld_3_UTR_plus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index5_Pld_3_UTR_plus_piRNA_1st_Sample_index5_Pld_3_UTR_plus_piRNA_1st*fastq &
cat Sample_index6_Pld_3_UTR_plus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index6_Pld_3_UTR_plus_piRNA_2nd_Sample_index6_Pld_3_UTR_plus_piRNA_2nd*fastq &
cat Sample_index7_Pld_3_UTR_minus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index7_Pld_3_UTR_minus_piRNA_1st_Sample_index7_Pld_3_UTR_minus_piRNA_1st*fastq &
cat Sample_index8_Pld_3_UTR_minus_piRNA_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index8_Pld_3_UTR_minus_piRNA_2nd_Sample_index8_Pld_3_UTR_minus_piRNA_2nd*fastq &
cat Sample_index9_42AB_start_plus_piRNA_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_index9_42AB_start_plus_piRNA_1st_Sample_index9_42AB_start_plus_piRNA_1st*fastq &
cat Sample_UBIG_320_FlamPro_deletion_1st/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1st.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1st*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1sttrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1sttrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1sttrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1stFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_1st_Sample_UBIG_320_FlamPro_deletion_1st*fastq &
cat Sample_UBIG_320_FlamPro_deletion_2nd/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2nd.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2nd*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndtrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndtrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndtrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2ndFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_UBIG_320_FlamPro_deletion_2nd_Sample_UBIG_320_FlamPro_deletion_2nd*fastq &
cat Sample_19294Index__5_CG13741_KD_piRNA_1/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19294Index__5_CG13741_KD_piRNA_1_Sample_19294Index__5_CG13741_KD_piRNA_1*fastq &
cat Sample_19295Index__6_CG13741_control/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_control.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_control*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlall.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlFastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlFastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlFastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlall.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlFastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlall.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controltrimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controltrimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controltrimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlalltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlalltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlallfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlallfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlFastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlalltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlallfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlallfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_controlFastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19295Index__6_CG13741_control_Sample_19295Index__6_CG13741_control*fastq &
cat Sample_19296Index__7_CG13741_KD_piRNA_2/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19296Index__7_CG13741_KD_piRNA_2_Sample_19296Index__7_CG13741_KD_piRNA_2*fastq &
cat Sample_19297Index__8_CG13741_control_piRNA_2/*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2.fastq && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2*.fastq > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2all.fastq && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2FastQCk6 && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2FastQCk6/Unique && mkdir -p /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2FastQCk6/Multi && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2all.fastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2FastQCk6 -k 6 && ~/.local/bin/cutadapt -a AAGATCGGAAGAGCACACGTCT /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2all.fastq  > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2trimmedfastq && java -jar /woldlab/castor/proj/programs/Trimmomatic-0.33/trimmomatic-0.33.jar SE -threads 4 -trimlog /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2trimmomatic.log /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2trimmedfastq /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2alltrimmedfastq ILLUMINACLIP:/woldlab/castor/home/phe/genomes/AllAdaptors.fa:2:30:10 MAXINFO:35:0.9 MINLEN:20 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2alltrimmedfastq -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 23 && length($2) <= 29' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2allfastq23_29 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2allfastq23_29 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2FastQCk6 -k 6 && cat /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2alltrimmedfastq | paste - - - - | awk -F"\t" 'length($2) >= 21 && length($2) <= 22' | sed 's/\t/\n/g' > /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2allfastq21_22 && /woldlab/castor/proj/programs/FastQC-0.11.3/fastqc /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2allfastq21_22 -o /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2FastQCk6 -k 6 && rm /woldlab/loxcyc/home/phe/210925YichengReprocess/Sample_19297Index__8_CG13741_control_piRNA_2_Sample_19297Index__8_CG13741_control_piRNA_2*fastq &
#for the following part: move the folder to public_html, then copy paste the following codes to run
These are bigWig tracks:
******************
current_folder_name=$(pwd|cut -d '/' -f7-)
    for file in *.bigWig
        do
            echo "track type=bigWig name="$file" description="$file" maxHeightPixels=60:32:8 visibility=full color=150,0,150 bigDataUrl=http://woldlab.caltech.edu/~phe/"$current_folder_name"/"$file >> tracksummary
        done