Changes between Version 31 and Version 32 of SOPs/chip_seq_peaks

Timestamp:

09/28/16 10:57:29 (8 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -43 +43 @@
 {{{
 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 BAM -g mm -n Name -B -p 1e-3 
+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 
 }}}
   * --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
+  * -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