ATAC-seq macs2 peak splitting in sliding windows

[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?

[jennaj]

Welcome @nancy

Sorry for the delayed reply. Try reviewing your methods to those in the GTN tutorial that covers ATAC-seq analysis:

ATAC-seq analysis and tutorial

Hi there, I’m following the tutorial for ATAC-seq analysis for the platform. They use Genrich for peak calling but it doesn’t show up when I look for it in “tools”. Isn’t it available yet? Thanks!