Question: Differential Peak Expression in ATAC-seq data
1
gravatar for ccag
3.7 years ago by
ccag30
Boston, MA
ccag30 wrote:

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?

ADD COMMENTlink modified 2.3 years ago by phosphodiester_bond40 • written 3.7 years ago by ccag30

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.

ADD REPLYlink written 3.7 years ago by geek_y11k
1
gravatar for phosphodiester_bond
2.3 years ago by
phosphodiester_bond40 wrote:

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

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

ADD COMMENTlink written 2.3 years ago by phosphodiester_bond40
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