Question: Calling differential peaks on ATAC-seq data
gravatar for ldyer2006
23 months ago by
ldyer200630 wrote:

My lab has recently run an ATAC-seq analysis on 3 biological conditions (Day 0, day 1 and day 7) with two replicates assigned to each. Once the data is finally generated, I will need to use some differential peak calling software to identify regions of differential accessibility between the 3 conditions. So far, I've thought that MACS2 would be the best option for this (The bdgdiff tool), but after reading around, THOR seems like it may be easier to use and provide better results.

Can anyone give me some advice about the potential benefits or limitations of using these two programs with ATAC-seq data?

thor atac-seq macs2 peak calling • 3.3k views
ADD COMMENTlink written 23 months ago by ldyer200630


For ATAC-seq I have used MACS2 for peak calling, followed by edgeR to see if peaks are different between groups. edgeR works for counts data, which ATAC-seq data is when you count all the reads that map to the peak regions.

ADD REPLYlink modified 23 months ago • written 23 months ago by b.nota6.0k

Have you completed this? I am trying to figure out how to do it now.

Check out this post: What are the best tools for differential detection between ATAC-seq samples?

I have used MACS2 and it took a while to get my head around it for ATAC but actually it turned out great. I have 4 conditions (each condition has 8 time points).

So now I am looking into getting differential expression.

Did you get your answer? - if so, what do you suggest, and what links were the biggest help?


ADD REPLYlink written 23 months ago by YaGalbi1.4k
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