Bowtie Template
Executable = /proj/genome/programs/bowtie-0.12.1/bowtie Arguments = /proj/genome/programs/bowtie-0.12.1/indexes/hg19sp75spike -v 2 -k 11 -m 10 --best --strata -p 4 -q /full/path/to/fastq_file/1184_1_1.fastq --un /full/path/to/unmapped_file/1184_1_1.unmapped.fa --max /full/path/to/repeats_file/1185_1_1.repeat.fa /full/path/to/output_file/1184_1_1.bowtie.txt Log = bowtie-submit.log.$(Process) Output = bowtie-submit.out.$(Process) Error = bowtie-submit.err.$(Process) request_cpus = 4 request_memory = 8000 request_disk = 0 Queue