How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect?
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26 days ago
mrj ▴ 70

I have processed my ATAC-seq reads and finally obtained MACs2 output bed files. I am at a loss to proceed from here to DESeq2 analysis. I will be thankful to you if could briefly explain the way to process the reads to use them for DESeq2 analysis.

DESEQ2 ATAC-Seq intersect bedtools MACS2 • 323 views
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Take a look at the DiffBind R package (which internally uses DESeq2, or edgeR), the tutorial vignette is quite extensive.

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Thank you so much!

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