Changes between Version 50 and Version 51 of SOPs/atac_Seq

Timestamp:

06/02/21 12:00:23 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -140 +140 @@
 
   # Call peaks: ENCODE uses very small p-value, so it could get enough peaks for IDR
-  # If you don't do IDR, you need to make p-value more stringent, such as with q 0.01
+  # If you don't run IDR, you need to make p-value more stringent, such as with q 0.01
   macs2 callpeak -t tagAlign.gz -n foo.narrow -f BED -g ${species} -p 0.01 --nomodel --shift -75 --extsize 150 --call-summits --keep-dup all -B --SPMR --call-summits
 
@@ -146 +146 @@
 
 
-  * Using pair-end bed as macs2 input. [[ https://twitter.com/XiChenUoM/status/1336658454866325506 | It considers ends of both mates, focus on cutting/insertion sites enrichment in ATAC-seq ]]. Codes implemented in the ATAC-seq review paper ( https://github.com/alexyfyf/atac_nf/blob/7f996b7de0e349c5a10dbbd75b2c266339517a3b/atac.nf#L341 )
+  * Using pair-end bed as macs2 input. It considers ends of both mates, focus on cutting/insertion sites enrichment in ATAC-seq. [[ [[ https://twitter.com/XiChenUoM/status/1336658454866325506 | Explaination ]]. Codes implemented in the ATAC-seq review paper ( https://github.com/alexyfyf/atac_nf/blob/7f996b7de0e349c5a10dbbd75b2c266339517a3b/atac.nf#L341 )
  [[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1929-3 | From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis]]
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