How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect?

Question

[mrj]

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.

[Papyrus]

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

[mrj]

Thank you so much!