Changes between Version 65 and Version 66 of SOPs/atac_Seq

Timestamp:

06/15/21 14:42:38 (4 years ago)

Author:

ibarrasa

Comment:

--

SOPs/atac_Seq

@@ -171 +171 @@
 
 
-     * If you are working with other species or don't have replicates, you can run macs2 with pair-end bed as an input. It considers ends of both mates, focus on [[https://twitter.com/XiChenUoM/status/1336658454866325506|cutting/insertion sites enrichment in ATAC-seq]].
+     * 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]].
 {{{
 # convert bam to bed