Changes between Version 101 and Version 102 of SOPs/atac_Seq

Timestamp:

01/27/22 12:18:13 (3 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -162 +162 @@
            * 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
-Follow this for species other other than human and mouse
-     * 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]].
+Follow this for species other than human/mouse, or if no replicates
+     * 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]].
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 # convert bam to bed