Changes between Version 52 and Version 53 of SOPs/atac_Seq

Timestamp:

06/02/21 12:38:25 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -163 +163 @@
     * Which macs option?
        * 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.
-          * Shifting reads, pos. strand +4 and neg strand -5 (see recommendations below) may be needed as well to find //exact// cut sites.
-
 
 [[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]]