Differential Peak Expression in ATAC-seq data

Question

[ccag]

I was wondering if anyone had experience dealing with determining statistically significant peaks in ATAC-seq data? I have been using MACS2 called peaks, finding the peak counts, and using EdgeR. However, I am not convinced on the results. Does anyone else have experience performing this type of analysis?

[GouthamAtla]

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

If you just take the peaks given by MACS2, they tend to have noise.

Answer 1

[phosphodiester_bond]

You can try DAStk, a tool recently put out for that purpose:

https://biof-git.colorado.edu/dowelllab/DAStk