Changes between Version 43 and Version 44 of SOPs/atac_Seq

Timestamp:

06/01/21 13:18:59 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -129 +129 @@
 
 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
-
-
-}}}
+ENCODE pipeline macs2 code:
+{{{
+
+  # Create virtual SE file containing both read pairs
+  bedtools bamtobed -i filtered.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'| gzip -c > tagAlign.gz
+
+  # Call peaks: ENCODE using very small p-value, so it could get enough peaks for IDR
+  macs2 callpeak -t tagAlign.gz -n foo.narrow -f BED -g ${species} -p 0.01 --nomodel --shift -75 --extsize 150 --call-summits --keep-dup all -B --SPMR --call-summits
+
+}}}
+
+MACS2 Commands used in ATAC-seq review paper: 
+{{{
+    # convert bam to bed
+    bedtools bamtobed -i $bam > ${name}_pe.bed 
+    macs2 callpeak -t ${name}_pe.bed -n ${name}_narrow -f BED -g ${species} -q 0.01 --nomodel --shift -75 --extsize 150 --call-summits --keep-dup all
+  
+}}}
+
+
+