How can I filter/extract called peaks based on their peak height?

Question

[jiekwo1]

Hello everyone,

So I am working with ATAC-seq data and wondering if there is a way to extract peaks that are above a certain threshold. For example, I want to extract peaks that are above the red line shown in the picture. Is this something I need to do at the time of peak calling? or can it be done after peak calling?

I am very new to ATAC-seq field so it's difficult to phrase what I am looking for into the right sentence. so please bear with me.

For your information, I just have bed and bigwig files.

If anyone could walk me through how to do that, I would greatly appreciate it!

All the best,

[ATpoint]

Technically you could do this based on some custom scripting that first extract the summit coverage and then subsets the peaks but that is cumbersome. I would rather filter for significance as peak height and width alone is influenced by a number of factors including technical ones such as mappability and GC content of the underlying DNA sequence. If you find that macs2 produces many small non-sensish peaks then yes I agree, that is why I abandoned it for ATAC-seq. I mean, it was developed for ChIP-seq where you had a lot more noise compared to the relatively clean ATAC-seq data. I like the Genrich peak caller, see https://github.com/jsh58/Genrich. You can set parameter for minimal peak length, AUC, and significance and it even can take replicated samples.

[jiekwo1]

thanks for your reply! I am going to try Genrich.