Differential Peak Expression in ATAC-seq data
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?
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phosphodiester_bond •
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ccag •
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ccag •
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You can try DAStk, a tool recently put out for that purpose:
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If you just take the peaks given by MACS2, they tend to have noise.