Changes between Version 61 and Version 62 of SOPs/atac_Seq

Timestamp:

06/15/21 12:45:23 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -176 +176 @@
      * If you are working with other species or don't have replicates, you can run macs2 with pair-end bed as an input. It considers ends of both mates, focus on [[https://twitter.com/XiChenUoM/status/1336658454866325506|cutting/insertion sites enrichment in ATAC-seq]].
 {{{
-    # convert bam to bed
-    bedtools bamtobed -i foo.bam > foo_pe.bed 
-    # shift reads
-    cat foo.pe.bed | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' >| foo_tn5_pe.bed
-    # call peaks. 
-    # --keep-dup all: since duplicates have been removed in previous step
-    macs2 callpeak -t foo_tn5_pe.bed -n foo -f BED -g mm -q 0.01 --nomodel --shift -75 --extsize 150 --call-summits --keep-dup all
+# convert bam to bed
+bedtools bamtobed -i foo.bam > foo_pe.bed 
+# shift reads
+cat foo.pe.bed | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' >| foo_tn5_pe.bed
+# call peaks. 
+# --keep-dup all: since duplicates have been removed in previous step
+macs2 callpeak -t foo_tn5_pe.bed -n foo -f BED -g mm -q 0.01 --nomodel --shift -75 --extsize 150 --call-summits --keep-dup all
   
 }}}
@@ -191 +191 @@
 
 {{{
-    macs2 callpeak -f BAMPE -t NFR.bam  --keep-dup all -B -q 0.01 -g mm -n MACS_ATACSeq_Peaks
+macs2 callpeak -f BAMPE -t NFR.bam  --keep-dup all -B -q 0.01 -g mm -n MACS_ATACSeq_Peaks
 }}}
 
@@ -197 +197 @@
 {{{
 
-   macs2 callpeak -t $foo.bam -f BAM -B -q 0.01 -g hs -n foo --nomodel --shift -75 --extsize 150
+macs2 callpeak -t $foo.bam -f BAM -B -q 0.01 -g hs -n foo --nomodel --shift -75 --extsize 150
 }}}