Changes between Version 82 and Version 83 of SOPs/chip_seq_peaks

Timestamp:

04/24/25 09:41:23 (10 hours ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -61 +61 @@
   * [[https://github.com/taoliu/MACS|MACS2]] is appropriate for both proteins like transcription factors that may have narrow peaks, as well as histone modifications that may affect broader regions. For broader peaks we recommend using --nomodel,--broad,  --nolambda (if there's no control), and using the fragment size calculated on the strand cross correlation analysis.  We recommend using macs2 rather than macs14 for broad peaks.  Identifying reproducible peaks (across replicates) with IDR requires MACS2 and works best with a relaxed p-value threshold.
 {{{
-bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -g mm -n Name -B -f BAM   --keep-dup auto --nomodel --extsize "size calculated on the strand crosscorrelation analysis"
-bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -g mm -n Name -B -f BAMPE --keep-dup 1    -p 1e-3 
+sbatch --partition=20 --job-name=MACS2 --mem=32G --wrap "macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -g mm -n Name -B -f BAM   --keep-dup auto --nomodel --extsize "size calculated on the strand crosscorrelation analysis" "
+sbatch --partition=20 --job-name=MACS2 --mem=32G --wrap "macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -g mm -n Name -B -f BAMPE --keep-dup 1 -p 1e-3"
 }}}
   * -B create bedgraph output files
@@ -99 +99 @@
 
 {{{ 
-bsub "sort -k 8,8nr IP.1_vs_control.1_peaks.narrowPeak | head -n 100000 | gzip -c >| IP.1_vs_control.1.regionPeak.gz"
-bsub "sort -k 8,8nr IP.2_vs_control.2_peaks.narrowPeak | head -n 100000 | gzip -c >| IP.2_vs_control.2.regionPeak.gz"
+sbatch --partition=20 --job-name=sort --mem=32G --wrap "sort -k 8,8nr IP.1_vs_control.1_peaks.narrowPeak | head -n 100000 | gzip -c >| IP.1_vs_control.1.regionPeak.gz"
+sbatch --partition=20 --job-name=sort --mem=32G --wrap "sort -k 8,8nr IP.2_vs_control.2_peaks.narrowPeak | head -n 100000 | gzip -c >| IP.2_vs_control.2.regionPeak.gz"
 }}}