Question: peaks overlap: ATAC & CHIP seq
0
gravatar for sophialovechan
2.9 years ago by
sophialovechan40 wrote:

Hi guys. I have two peak files. One is from ATAC seq and the other is from H3K27ac chip seq. I am trying to merge these two peaks files together and get a file with overlapping peaks. There are several questions that I have here:

  1. what scripts or programs are good for that application? (bedops and bedmap?)

  2. I used MACS2 to call peaks: regular peaks calling for ATAC seq and broad peaks calling for H3K27ac chip seq. I am concerned whether the different peak calling methods will influence the overlapping results. Thank you!

chip-seq • 3.9k views
ADD COMMENTlink modified 2.9 years ago by Alex Reynolds29k • written 2.9 years ago by sophialovechan40
1
gravatar for Satyajeet Khare
2.9 years ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k wrote:
  1. You can use bedtools intersect
  2. It should not matter much.
ADD COMMENTlink modified 2.9 years ago by Ian5.5k • written 2.9 years ago by Satyajeet Khare1.5k
1
gravatar for Alex Reynolds
2.9 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

You can use bedops to do the merging and bedmap to get a list of peaks that overlap the merged regions:

$ bedops --merge A.bed B.bed C.bed ... > merge.bed
$ bedops --everything A.bed B.bed C.bed ... > union.bed
$ bedmap --echo --echo-map merge.bed union.bed > answer.bed

Or as a one-liner:

$ bedmap --echo --echo-map <(bedops --merge A.bed B.bed C.bed ...) <(bedops --everything A.bed B.bed C.bed ...) > answer.bed
ADD COMMENTlink written 2.9 years ago by Alex Reynolds29k
0
gravatar for spacemorrissey
2.9 years ago by
United States
spacemorrissey230 wrote:

You may want to consider using Fseq to call ATAC seq peaks instead of MACS2. H3K27ac gives fairly punctate peaks, so you should probably be fine, but any time you are doing intersections you should consider the size of the peak regions from both sets, and decide if how you want to define the peak boundaries for the intersected set.

ADD COMMENTlink written 2.9 years ago by spacemorrissey230
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