Changes between Version 49 and Version 50 of SOPs/chip_seq_peaks

Timestamp:

03/04/20 10:35:04 (5 years ago)

Author:

thiruvil

Comment:

--

SOPs/chip_seq_peaks

@@ -49 +49 @@
 }}}
   * -B create bedgraph output files
-  * -f Input format (typically BAM for single-end reads and BAMPE for paired-end reads).  In BAMPE mode, MACS2 will only use properly-paired read alignments, see [[https://groups.google.com/forum/#!topic/macs-announcement/Vh916L3tOOE | MACS2 Forum ]].  
+  * -f Input format (typically BAM for single-end reads and BAMPE for paired-end reads).  In BAMPE mode, MACS2 will only use properly-paired read alignments, see [[https://groups.google.com/forum/#!topic/macs-announcement/Vh916L3tOOE | MACS2 Forum ]], also from the readme/manual, "when format BAMPE is specified, MACS will use the real fragments inferred from alignment results for reads pileup."  If you have PE ChIP-Seq data, -f bampe option is recommended.
   * --nomodel  whether or not to build the shifting model. If True, MACS will not build model. By default it means shifting size = 100.                      
   * --extsize When nomodel is true, MACS will use this value as fragment size to extend each read towards 3' end