Question: ATAC-seq macs2 peak splitting in sliding windows
gravatar for nancy
11 days ago by
nancy0 wrote:

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?

atac-seq • 83 views
ADD COMMENTlink modified 4 days ago by danvoronov10 • written 11 days ago by nancy0

What exactly is the problem?

ADD REPLYlink written 8 days ago by ATpoint23k
gravatar for danvoronov
4 days ago by
SZN, Naples, Italy
danvoronov10 wrote:

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

ADD COMMENTlink written 4 days ago by danvoronov10
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