ATAC-seq macs2 peak splitting in sliding windows

Question

[nancy]

I used macs2 to call peaks for atac-seq data. now my goal is to split the peaks into 50 bp windows with 25 bp steps and then calculate the Tn5 integration frequency in each window.

How should I proceed with that?

[ATpoint]

What exactly is the problem?

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Edit 26/9/19: Cross-posted => https://bioinformatics.stackexchange.com/questions/9365/atac-seq-macs2-peak-splitting-in-sliding-windows

Answer 1

[danvoronov]

Hello, you can use bedtools makewindows -b <your narrowpeak files from macs2> -w 50 -s 25 > <output file> this will give you the sliding windows you want.

The Tn5 integration frequency is unclear, because you should have the fragments generated by the transposase "cutting" the genome, so I think you need 2 transposase reactions to generate one fragment. Could you elaborate on what you need?

Best, Dan