Question: Differential Peak Expression in ATAC-seq data
1
gravatar for ccag
23 months 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 5 months ago by phosphodiester_bond20 • written 23 months 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 23 months ago by geek_y8.8k
1
gravatar for phosphodiester_bond
5 months ago by
phosphodiester_bond20 wrote:

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

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

ADD COMMENTlink written 5 months ago by phosphodiester_bond20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1832 users visited in the last hour