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.
Take a look at the DiffBind R package (which internally uses DESeq2, or edgeR), the tutorial vignette is quite extensive.
Thank you so much!
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