Changes between Version 9 and Version 10 of SOPs/atac_Seq

Timestamp:

08/11/20 14:00:21 (4 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -61 +61 @@
     * 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.
 
-  * Genrich is another piece of software for peak-calling. It has the advantage of running all of the post-alignment steps through peak-calling with one command. It can take multiple replicates. Detailed information can be found in [[https://informatics.fas.harvard.edu/atac-seq-guidelines.html|Harvard ATAC-seq Guidelines]] 
+  * [[https://github.com/jsh58/Genrich | Genrich]] is another piece of software for peak-calling. It has the advantage of running all of the post-alignment steps through peak-calling with one command. It can take multiple replicates. Detailed information can be found in [[https://informatics.fas.harvard.edu/atac-seq-guidelines.html|Harvard ATAC-seq Guidelines]] 
 
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