Changes between Version 87 and Version 88 of SOPs/atac_Seq

Timestamp:

07/09/21 16:48:50 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -152 +152 @@
 }}}
 
+     * The QC report is call-qc_report/execution/qc.html
+     * idr peaks files:
+           * rep1: call-idr_pr/shard-0/execution/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.gz
+           * rep2: call-idr_pr/shard-1/execution/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.gz
+           * Note: shard-0 refers to the first biological replicate, shard-1 refers to the 2nd biological replicate, and so on
+           * rep1 and rep2: call-idr/shard-1/execution/rep1_vs_rep2.idr0.05.bfilt.narrowPeak.gz
 
      * If you are working with other species or don't have replicates, you should run macs2 using pair-end bed as input and the options "--shift -75 --extsize 150". With those settings you will be creating a profile of reads around the cutting sites (one at each end of the fragment/paired read) that will result on peaks centered around the cutting sites (open chromatin). This is an important difference with ChIP-seq analysis. On ChIP-seq the binding event tends to be in the middle of the fragment; on ATAC-seq chromatin was opened where the cutting occurred and that is the end of the fragment. [[https://twitter.com/XiChenUoM/status/1336658454866325506|cutting/insertion sites enrichment in ATAC-seq]].