Changes between Version 7 and Version 8 of SOPs/atac_Seq

Timestamp:

08/11/20 11:23:18 (5 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -87 +87 @@
     * The nucleosome free region (NFR) should be > 38bp to < 147 bases (one nucleosome); mono nucleosome fragments are in the range of 147-200 bp
     * unless you have high coverage, e.g. ~50M reads or more, use all reads for downstream analysis and not remove mono-, di-, tri-, etc. nucleosome fragments or reads.  Otherwise, you may miss many open chromatin regions during peak calling.
+    * recommend at least ~50M reads/coverage for calling open/accessible regions, and ~200M reads for TF/footprinting.
   * check fragment size distribution (from ATACSeqQC)
     * see [[https://www.nature.com/articles/nmeth.2688/figures/2 | Fig 2]] from Buenrostro, J.D., et al. for expected distribution of fragment size
@@ -93 +94 @@
 
 
+=== Other Software/Reference ===
 
-
-* Other software: [[https://github.com/LiuLabUB/HMMRATAC | HMMRATAC]]
+* [[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1929-3 | From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis]]
+* software: [[https://github.com/LiuLabUB/HMMRATAC | HMMRATAC]]