Changes between Version 44 and Version 45 of SOPs/atac_Seq

Timestamp:

06/01/21 13:27:37 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -129 +129 @@
 
 MACS v2 is applicable for ATAC-Seq using the appropriate options/parameters. 
-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: 
+
+MACS2 [[ https://github.com/alexyfyf/atac_nf/blob/7f996b7de0e349c5a10dbbd75b2c266339517a3b/atac.nf#L341 | commands used in ATAC-seq review paper ]]: [[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1929-3 | From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis]]
 {{{
     # convert bam to bed
@@ -148 +138 @@
 }}}
 
-
-
-
-
-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.
-{{{
-
-macs2 callpeak -f BAMPE -t file.sorted.bam  --keep-dup 1 -B -q 0.01 -g mm -n MACS_ATACSeq_Peaks
-
+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 uses 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
+
+}}}
+
+
+If using the 'BAMPE' option with paired-end reads, let MACS run the pileup and calculate 'extsize'; 
 #note: if duplicates were removed, use --keep-dup all; if not, use --keep-dup 1.  Removing duplicates is recommended.
+{{{
+
+macs2 callpeak -f BAMPE -t file.sorted.bam  --keep-dup all -B -q 0.01 -g mm -n MACS_ATACSeq_Peaks
+
+
 
 #BAMPE format: there is no special format for BAMPE - MACS will treat PE reads as coming from the same fragment, from the manual,