How to quantify the reads of peaks?

Question

[Dan]

Hello

I have the peaks file from macs2 output, I want to quantify how many reads of each peak from the bam file. Is there a package or bash/R/Python code that can do this quantification?

Thanks

Answer 1

[jared.andrews07]

Plenty of options - DiffBind, csaw among two of the more accessible.

Answer 2

[heritabilities]

Lots of great information on this site and even a few published best-practices depending on your ultimate goal.

Best practices for differential accessibility with ATACseq here, which includes some R scripts for using csaw and lots of great background.

You could also quantify peaks directly from bam files directly.

In any case, if you are assessing differential accessibility between conditions, ensure you at least consider normalization to account for differences in library output. Deciding how to define consensus peaks across conditions also dramatically impacts DA calls (see Reske et al 2020).