Changes between Version 32 and Version 33 of SOPs/atac_Seq

Timestamp:

02/18/21 09:39:35 (4 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -134 +134 @@
 }}}
 
-Additional notes on calling peaks using MACS: using MACS default options without BAMPE may not call the correct peaks.  Alternative options/parameters in calling peaks using MACS, if BAMPE is not used are, --nomodel --shift s --extsize 2s, this can be used for single-end reads as well, e.g. --shift 100 --extsize 200 is suitable for ATAC-Seq.   
+Additional notes on calling peaks using MACS: ''using MACS default options without BAMPE will not call the correct peaks''.  Alternative options/parameters in calling peaks using MACS, if BAMPE is not used are, --nomodel --shift s --extsize 2s, this can be used for single-end reads as well, e.g. --shift 100 --extsize 200 is suitable for ATAC-Seq.   
     * MACS' author, T.Liu, recommends using -f BAMPE if PE reads are used [[https://github.com/taoliu/MACS/issues/331]], using BAMPE option asks MACS to pileup and calculate the extension size -  works for finding accessible regions within cut sites.  The additional parameters can also be used to look only at the //exact// cut sites by Tn5 instead of the open/accessible regions [[https://github.com/taoliu/MACS/issues/145]], if so, -f BAMPE may not be suitable.
+    * another approach is to convert the bam file to bed (using bedtools), and use the options, -f BED --shift 100 --extsize 200
 
 [[https://github.com/jsh58/Genrich | Genrich]] is another piece of software for peak-calling. It has the advantages of (a) running all of the post-alignment steps through peak-calling with one command, and (b) can process multiple replicates. Detailed information can be found in [[https://informatics.fas.harvard.edu/atac-seq-guidelines.html|Harvard ATAC-seq Guidelines]]