Question: ATAC-seq macs2 peak splitting in sliding windows
0
gravatar for nancy
11 days ago by
nancy0
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
1
gravatar for danvoronov
4 days ago by
danvoronov10
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 882 users visited in the last hour