Changes between Version 41 and Version 42 of SOPs/atac_Seq

Timestamp:

05/27/21 09:35:39 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -128 +128 @@
 === [=#call_peaks Call peaks] ===
 
-MACS v2 is applicable for ATAC-Seq using the appropriate options/parameters.
+MACS v2 is applicable for ATAC-Seq using the appropriate options/parameters. 
+{{{
+  # Convert alignment bam file to bed
+
+  # Shift reads: reads aligning to the + strand offset by +4 bp; reads aligning to the – strand offset −5 bp
+
+  # Call peaks
+  macs2 callpeak -t pe.bed -n foo.narrow -f BED -g ${species} -q 0.01 --nomodel --shift -75 --extsize 150 --call-summits --keep-dup all
+
+
+}}}
+
 
 If using the 'BAMPE' option with paired-end reads, let MACS run the pileup and calculate 'extsize'; ask MACS to keep only 1 read if duplicates are present.