Differential Peak Expression in ATAC-seq data
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4.3 years ago
ccag ▴ 30

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?

ATAC-seq peak calling differential expression • 7.5k views
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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.

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2.9 years ago

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

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

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