Changes between Version 36 and Version 37 of SOPs/atac_Seq

Timestamp:

03/16/21 11:54:39 (4 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -239 +239 @@
   * Unless you have high coverage, 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.
   * 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.
+    * Shorter reads lengths to sequence NFR/fragments, e.g. 50x50 or 75x75, should be used instead of longer reads, e.g. 100x100.
   * For calling open/accessible regions, at least ~50M reads are recommended.
-  * For transcription factor footprinting, at least ~200M reads are recommended.
+  * For transcription factor footprinting, at least ~200M reads are recommended to ensure high coverage of the NFR.
   * Tn5 produces 5’ overhangs of 9 bases long: pos. strand + 4 and neg strand -5 (shiftGAlignmentsList and shiftReads function) splitGcAlignmentsByCut: creates different bins of reads: NFR, mono, di, etc. Shifted reads that do not fit into any of the bins should be discarded.
   * Use housekeeping genes to check QC: signal enrichment is expected in the regulatory regions of housekeeping genes in good ATAC-seq experiments. Use IGVSnapshot function with geneNames param. splitGAlignmentsByCut: creates different bins of reads: NFR, mono, di, etc. Shifted reads that do not fit into any of the bins should be discarded.