Changes between Version 43 and Version 44 of SOPs/chip_seq_peaks

Timestamp:

11/14/17 09:27:57 (7 years ago)

Author:

thiruvil

Comment:

--

SOPs/chip_seq_peaks

@@ -43 +43 @@
 ==== MACS2 ====
 
-  * 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.
+  * [[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"
@@ -66 +66 @@
   * -log10(qvalue) at peak summit
 
+[[https://github.com/taoliu/MACS/wiki | MACS2 wiki]] 
 
 ==== MACS14 ====