Changes between Version 32 and Version 33 of SOPs/SAMBAMqc

Timestamp:

10/28/25 16:11:27 (6 days ago)

Author:

kdesilva

Comment:

--

SOPs/SAMBAMqc

@@ -50 +50 @@
    # output: CollectInsertSizeMetrics.txt: values for -r and --mate-std-dev can be found in this text file
    #         CollectInsertSizeMetrics_hist.pdf: insert size histogram (graphic representation)
-bsub java -jar /usr/local/share/picard-tools/picard.jar CollectInsertSizeMetrics I=foo.bam O=CollectInsertSizeMetrics.txt H=CollectInsertSizeMetrics_hist.pdf
+sbatch --partition=20 --job-name=picard_insert --mem=8G --wrap "java -jar /usr/local/share/picard-tools/picard.jar CollectInsertSizeMetrics I=foo.bam O=CollectInsertSizeMetrics.txt H=CollectInsertSizeMetrics_hist.pdf"
 }}}
 
@@ -84 +84 @@
 # Before submitting to cluster
 unset DISPLAY  
-bsub "qualimap bamqc -bam myFile.bam -outdir output_qualimap"
+sbatch --partition=20 --job-name=qualimap_bamqc --mem=8G --wrap "qualimap bamqc -bam myFile.bam -outdir output_qualimap"
 # For huge data, you can increase memory with --java-mem-size="4800M" to avoid OutOfMemoryError: Java heap space
 
 # For rnaseq QC
-bsub "qualimap rnaseq -bam myFile.bam -gtf Homo_sapiens.GRCh37.72.canonical.gtf -outdir output_qualimap_rnaseq -p non-strand-specific"
+sbatch --partition=20 --job-name=qualimap_rnaseqqc --mem=8G --wrap "qualimap rnaseq -bam myFile.bam -gtf Homo_sapiens.GRCh37.72.canonical.gtf -outdir output_qualimap_rnaseq -p non-strand-specific"
 
 # For counts QC (after using htseq-count or a similar program to generate a matrix of counts)
@@ -106 +106 @@
 bam_stat.py -i myFile.bam
 # Or run on a folder of BAMs
-for bamFile in `/bin/ls *.bam`; do bsub "bam_stat.py -i $bamFile > $bamFile.bam_stat.txt"; done
+for bamFile in `/bin/ls *.bam`; do sbatch --partition=20 --job-name=bamstat_${bamFile%.bam} --mem=4G --wrap "bam_stat.py -i $bamFile > $bamFile.bam_stat.txt"; done
 }}}
 ==== Use infer_experiment.py from the RseQC package to check if/how your RNA-seq reads are stranded. ====
@@ -113 +113 @@
 # Command line:
 
-bsub "infer_experiment.py -i My_sample.accepted_hits.bam -r my_genes.bed > My_sample.infer_experiment.out.txt"
+sbatch --partition=20 --job-name=infer_exp --mem=4G --wrap "infer_experiment.py -i My_sample.accepted_hits.bam -r my_genes.bed > My_sample.infer_experiment.out.txt"
 
 -i INPUT_FILE in SAM or BAM format
@@ -198 +198 @@
 {{{
 # Usage: ./dupRadar.R <file.bam> <genes.gtf> <stranded=[no|yes|reverse]> paired=[yes|no] outdir=./ threads=1
-bsub /nfs/BaRC_Public/BaRC_code/R/dupRadar/dupRadar.R WT.bam /nfs/genomes/mouse_mm10_dec_11_no_random/gtf/Mus_musculus.GRCm38.81.canonical.gtf stranded=no paired=yes outdir=dupRadar_out threads=1
+sbatch --partition=20 --job-name=dupRadar --mem=8G --wrap "/nfs/BaRC_Public/BaRC_code/R/dupRadar/dupRadar.R WT.bam /nfs/genomes/mouse_mm10_dec_11_no_random/gtf/Mus_musculus.GRCm38.81.canonical.gtf stranded=no paired=yes outdir=dupRadar_out threads=1"
 }}}