Changes between Version 32 and Version 33 of SOPs/chip_seq_peaks

Timestamp:

09/28/16 11:32:42 (8 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -42 +42 @@
   * 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 --extsize "size calculated on the strand croscorrelation analysis"
-bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -f BAMPE -g mm -n Name -B -p 1e-3 
-}}}
+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 
+}}}
+  * -B create bedgraph output files
+  * -f Input format (typically BAM for single-end reads and BAMPE for paired-end reads)
   * --nomodel  whether or not to build the shifting model. If True, MACS will not build model. By default it means shifting size = 100.                      
-  * -f Input format (typically BAM for single-end reads and BAMPE for paired-end reads)
-  * -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
+  * --keep-dup How should MACS handle duplicate tags at the same location?  The default is to keep just one.  The 'auto' option (recommended for high-coverage samples) has MACS calculate the expected maximum tags at the same location (based on the binomal distribution).
   * For future IDR analysis, use '-p 1e -3' => Set p-value cutoff to 1e-3 (which is more relaxed than the default setting)