Changes between Version 15 and Version 16 of SOPs/chip_seq_peaks

Timestamp:

03/25/15 16:49:49 (10 years ago)

Author:

ibarrasa

Comment:

--

SOPs/chip_seq_peaks

@@ -39 +39 @@
   * 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 -f BAM -g mm -n Name --nomodel -B
+bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -f BAM -g mm -n Name --nomodel -B --extsize "size calculated on te strand croscorrelation analysis"
 bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -f BAM -g mm -n Name -B -p 1e-3 
 }}}
@@ -45 +45 @@
   * -f Input format
   * -B create bedgraph output files
+  * --extsize When nomodel is true, MACS will use this value as fragment size to extend each read towards 3' end
   * For future IDR analysis, use '-p 1e -3' => Set p-value cutoff to 1e-3 (which is more relaxed than the default setting)