Changes between Version 69 and Version 70 of SOPs/atac_Seq

Timestamp:

07/08/21 12:33:58 (4 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -300 +300 @@
   * 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.
-  * 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.
+  * 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.
+  * 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. 
 
 === Further reading ===