ChIP-Seq Analysis: Comparing Unannotated Peaks with DESeq2
Entering edit mode
vanbelj ▴ 20
Last seen 17 days ago
United States

I typically use DESeq2 to compare a Salmon-generated counts table, wherein counts are binned into pre-annotated regions (e.g. Gene A, Gene B, etc..). Binning in this manner has its limitations. For instance, if multiple peaks exist within a given annotation and Condition A causes a loss of one peak but retains the others, a difference may not be identified.

As a next step, I would like to use an undirected peak calling method, such as MACS2, to identify peaks in my dataset. These peaks would then represent annotations into which Salmon binned reads and which DESeq2 then analyzed for differences into counts.

I'm sure what I'm describing has been done by many, and I am hoping someone here might be able to direct me to a technical guide. I am especially unsure of how to link MACS2 peaks back to annotations to give them some relevance.

Thanks for any help!

DESeq2 MACS2 • 755 views
Entering edit mode
ATpoint ★ 3.9k
Last seen 10 hours ago

If you want a window-based analysis you can use csaw:

Entering edit mode

A few years ago when I first started this sort of analysis I did attempt to use csaw but was not successful. I can't recall if it was a coding issue or if the amount of background signal from my technique caused issues. I am analyzing ChEC-seq data, which does tend to yield more background signal across the genome. I'm also working in budding yeast (can't remember if genome was available for csaw).

I'll revisit and see if I can get it to run.


Login before adding your answer.

Traffic: 474 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6