Changes between Version 51 and Version 52 of SOPs/miningSAMBAM

Timestamp:

08/08/24 11:50:35 (5 months ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -44 +44 @@
 /nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl
 # Or on a folder of SAM files
-for samFile in `/bin/ls *.sam`; do bsub /nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl $samFile ; done
+for samFile in `/bin/ls *.sam`; do sbatch --partition=20 --job-name=sam2bam --mem=32G --wrap "/nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl $samFile " ; done
 }}}
 
@@ -167 +167 @@
 Tophat/bowtie mappers create the tag NH:i:XXX where XXX is the number of times the read has mapped.
 {{{
-bsub "samtools view accepted_hits.bam | grep -v NH:i:1 | perl -pe 's/AS.+(NH:i:\d+)/\$1/' | cut -f1,10,12 | perl -pe 's/NH:i://' | sort -u -k3,3nr > Multi-mapped.sorted.txt"
+sbatch --partition=20 --job-name=samtools --mem=32G --wrap "samtools view accepted_hits.bam | grep -v NH:i:1 | perl -pe 's/AS.+(NH:i:\d+)/\$1/' | cut -f1,10,12 | perl -pe 's/NH:i://' | sort -u -k3,3nr > Multi-mapped.sorted.txt"
 # Output format:
 # read_ID<tab>read<tab>number times mapped
@@ -186 +186 @@
 #               accepted_hits_posStrand.bam: mapped to positive strand
 
-bsub "samtools view -f 16 -b accepted_hits.bam >| accepted_hits_negStrand.bam"
-bsub "samtools view -F 16 -b accepted_hits.bam >| accepted_hits_posStrand.bam"
+sbatch --partition=20 --job-name=samtools --mem=32G --wrap "samtools view -f 16 -b accepted_hits.bam >| accepted_hits_negStrand.bam"
+sbatch --partition=20 --job-name=samtools --mem=32G --wrap "samtools view -F 16 -b accepted_hits.bam >| accepted_hits_posStrand.bam"
 
 }}}
@@ -196 +196 @@
 # output:       1st pair: accepted_hits_1stPair.bam
 #               2nd pair: accepted_hits_2ndPair.bam
-bsub "samtools view -b -f 0x0040 accepted_hits.bam > accepted_hits_1stPair.bam"
-bsub "samtools view -b -F 0x0040 accepted_hits.bam > accepted_hits_2ndPair.bam"
+sbatch --partition=20 --job-name=samtools --mem=32G --wrap "samtools view -b -f 0x0040 accepted_hits.bam > accepted_hits_1stPair.bam"
+sbatch --partition=20 --job-name=samtools --mem=32G --wrap "samtools view -b -F 0x0040 accepted_hits.bam > accepted_hits_2ndPair.bam"
 }}}
 
@@ -243 +243 @@
 qualimap bamqc -bam Mapped_DNA_reads.bam -outdir qualimap_output -outformat PDF:HTML
 # Command-line execution may require disabling X-windows
-bsub "unset DISPLAY; qualimap bamqc -bam Mapped_DNA_reads.bam -outdir qualimap_output -outformat PDF:HTML"
+sbatch --partition=20 --job-name=bamqc --mem=32G --wrap "unset DISPLAY; qualimap bamqc -bam Mapped_DNA_reads.bam -outdir qualimap_output -outformat PDF:HTML"
 }}}