Changes between Version 89 and Version 90 of SOPs/atac_Seq

Timestamp:

08/04/21 14:20:59 (4 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -329 +329 @@
   * The nucleosome free region (NFR) should be > 38bp to < 147 bases (one nucleosome); mono nucleosome fragments are in the range of 147-200 bp
     * Shorter reads lengths, e.g. 50x50 or 75x75, should be used instead of longer reads, e.g. 100x100 or longer, to ensure NFR/fragments are sequenced
-  * For calling open/accessible regions, at least ~50M reads are recommended.
-  * For transcription factor footprinting, at least ~200M reads are recommended to ensure high coverage of the NFR.
+  * ATAC-Seq depth or coverage:
+    * calling open/accessible regions, at least ~50M reads are recommended
+    * transcription factor footprinting, at least ~200M reads are recommended or optimal to ensure high coverage of the NFR
   * Tn5 produces 5’ overhangs of 9 bases long: pos. strand +4 and neg strand -5 (see shiftGAlignmentsList and shiftReads functions in ATACseqQC package)
     *  splitGAlignmentsByCut (in ATACseqQC package): creates different bins of reads, e.g. NFR, mono, di, etc. Shifted reads that do not fit into any of the bins should be discarded.