Changes between Version 33 and Version 34 of SOPs/chip_seq_peaks

Timestamp:

09/29/16 14:51:03 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/chip_seq_peaks

@@ -46 +46 @@
 }}}
   * -B create bedgraph output files
-  * -f Input format (typically BAM for single-end reads and BAMPE for paired-end reads)
+  * -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 ]].  
   * --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