Changes between Version 9 and Version 10 of SOPs/coordinates

Timestamp:

10/30/25 16:43:55 (3 days ago)

Author:

kdesilva

Comment:

--

SOPs/coordinates

@@ -188 +188 @@
 #               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 --job-name=samtools_negStrand --mem=4G --wrap="samtools view -f 16 -b accepted_hits.bam >| accepted_hits_negStrand.bam"
+sbatch --job-name=samtools_posStrand --mem=4G --wrap="samtools view -F 16 -b accepted_hits.bam >| accepted_hits_posStrand.bam"
 
 }}}
@@ -198 +198 @@
 # output:       1st pair: *_1stPair.bam
 #                       2nd pair: *_2ndPair.bam
-bsub "samtools view -b -f 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_1stPair.bam"
-bsub "samtools view -b -F 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_2ndPair.bam"
-bsub "samtools view -b -f 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_1stPair.bam"
-bsub "samtools view -b -F 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_2ndPair.bam"
+sbatch --job-name=samtools_pos_1st --mem=4G --wrap="samtools view -b -f 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_1stPair.bam"
+sbatch --job-name=samtools_pos_2st --mem=4G --wrap="samtools view -b -F 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_2ndPair.bam"
+sbatch --job-name=samtools_neg_1st --mem=4G --wrap="samtools view -b -f 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_1stPair.bam"
+sbatch --job-name=samtools_neg_1st --mem=4G --wrap="samtools view -b -F 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_2ndPair.bam"
 }}}
 
@@ -210 +210 @@
 #                                   chr1    197195432
 # output:       bedgraph format: accepted_hits_*Strand_*Pair.bedgraph
-bsub "genomeCoverageBed -split -bg -ibam accepted_hits_posStrand_1stPair.bam -g mm9.size >| accepted_hits_posStrand_1stPair.bedgraph"
-bsub "genomeCoverageBed -split -bg -ibam accepted_hits_posStrand_2ndPair.bam -g mm9.size >| accepted_hits_posStrand_2ndPair.bedgraph"
-bsub "genomeCoverageBed -split -bg -ibam accepted_hits_negStrand_1stPair.bam -g mm9.size >| accepted_hits_negStrand_1stPair.bedgraph"
-bsub "genomeCoverageBed -split -bg -ibam accepted_hits_negStrand_2ndPair.bam -g mm9.size >| accepted_hits_negStrand_2ndPair.bedgraph"
+sbatch --job-name=gc_pos_1st --mem=8G --wrap="genomeCoverageBed -split -bg -ibam accepted_hits_posStrand_1stPair.bam -g mm9.size >| accepted_hits_posStrand_1stPair.bedgraph"
+sbatch --job-name=gc_pos_2nd --mem=8G --wrap="genomeCoverageBed -split -bg -ibam accepted_hits_posStrand_2ndPair.bam -g mm9.size >| accepted_hits_posStrand_2ndPair.bedgraph"
+sbatch --job-name=gc_neg_1st --mem=8G --wrap="genomeCoverageBed -split -bg -ibam accepted_hits_negStrand_1stPair.bam -g mm9.size >| accepted_hits_negStrand_1stPair.bedgraph"
+sbatch --job-name=gc_neg_2nd --mem=8G --wrap="genomeCoverageBed -split -bg -ibam accepted_hits_negStrand_2ndPair.bam -g mm9.size >| accepted_hits_negStrand_2ndPair.bedgraph"
 }}}
 
@@ -249 +249 @@
 # *output:      bigwig format: neg.bw or pos.bw
 #                       neg.bw or pos.bw can be visualized with IGV/UCSC genome browser
-bsub bedGraphToBigWig neg.bedgraph mm9.size_noHeader neg.bw
-bsub bedGraphToBigWig pos.bedgraph mm9.size_noHeader pos.bw
-}}}
+sbatch --job-name=bedGraphToBigWigneg --mem=2G --wrap="bedGraphToBigWig neg.bedgraph mm9.size_noHeader neg.bw"
+sbatch --job-name=bedGraphToBigWigpos --mem=2G --wrap="bedGraphToBigWig pos.bedgraph mm9.size_noHeader pos.bw"
+}}}