3 # This is no longer supported. It is recommended that the pythin script of the same name be used instead.
5 # runRNAPairedAnalysis.sh
8 # example: . ../commoncode/runRNAPairedAnalysis.sh mouse c2c12rna ../mm9repeats/rmask.db
10 # assuming that we have rds database with the prefix c2c12rna.24R and that an RNAFAR analysis has already been run.
12 # set ERANGEPATH to the absolute or relative path to ERANGE, if it's not in the environment
14 if [ -z "$ERANGEPATH" ]
16 ERANGEPATH='../erange'
19 echo 'runRNAPairedAnalysis.sh: version 3.8'
28 replacemodels=" --models $5 --replacemodels "
34 echo 'usage:runRNAPairedAnalysis.sh genome rdsprefix repeatmaskdb [modelfile] [--replacemodels]'
36 echo 'where rdsprefix is the name of the rds file without the .rds extension'
37 echo 'use "none" for the repeatmaskdb if you do not have one'
42 arguments=$1' '$2' '$3' '$models' '$5
43 echo 'running with settings: ' $arguments
44 python $ERANGEPATH/recordLog.py rna.log runRNAPairedAnalysis.sh "with parameters: $arguments"
46 # count the unique reads falling on the gene models ; the nomatch files are
47 # mappable reads that fell outside of the Cistematic gene models and not the
48 # unmappable of Eland (i.e, the "NM" reads)
49 echo "python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count -markGID -cache 1 $models $replacemodels"
50 python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count --markGID --cache 1 $models $replacemodels
52 # calculate a first-pass RPKM to re-weigh the unique reads,
53 # using 'none' for the splice count
54 python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.count none $2.firstpass.rpkm --cache $models $replacemodels
56 # recount the unique reads with weights calculated during the first pass
57 python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.firstpass.rpkm $2.uniqs.recount --uniq --cache 1 $models $replacemodels
60 python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count --splices --noUniqs --markGID --cache 1 $models $replacemodels
62 # find new regions outside of gene models with reads piled up
63 python $ERANGEPATH/findall.py RNAFAR $2.rds $2.newregions.txt --RNA --minimum 1 --nomulti --flag NM --log rna.log --cache 1
65 # filter out new regions that overlap repeats more than a certain fraction
66 python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.checked --startField 1 --log rna.log --cache 1
68 # calculate the read densities
69 python $ERANGEPATH/regionCounts.py $2.newregions.checked $2.rds $2.newregions.good --markRDS --cache --log rna.log
71 # map all candidate regions that have paired ends overlapping with known genes
72 python $ERANGEPATH/rnafarPairs.py $1 $2.newregions.good $2.rds $2.candidates.txt --cache $models $replacemodels
74 # calculate expanded exonic read density
75 python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.recount $2.splices.count $2.expanded.rpkm $2.candidates.txt $2.accepted.rpkm --cache $models $replacemodels
78 python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.expanded.rpkm $2.multi.count --accept $2.accepted.rpkm --multi --cache 1 $models $replacemodels
80 # calculate final exonic read density
81 python $ERANGEPATH/normalizeFinalExonic.py $2.rds $2.expanded.rpkm $2.multi.count $2.final.rpkm --multifraction --withGID --cache