Question: ChIP-seq differential peak calling (Any way to set the window size for calling differential enriched peaks?)
1
gravatar for chiefcat
4 months ago by
chiefcat70
chiefcat70 wrote:

Hi everyone. I'm analysing the H3K9me3 ChIP from the ChIP experiment I've conducted. However, the bioinformatic parts were did by a labmate who understand programming languages but lack of experience in analysing ChIP-seq.

We are now very struggling in calling the differential enriched peaks of my H3K9me3 ChIP between 2 conditions. The peaks were called by MACS2 either using default or --broad. Other parameters are as below. However, after calling the differential enriched peaks using bdgdiff, I found those "differential peaks" called are not as what I expected.

Question 1: Is there any way we can call the differential peaks based on the length of the broad peaks? In this way, it can tell if the histone mark is differentially enriched over a wide region (such as gene body).

Question 2: Sometimes, ChIP signal is actually enriched over a broad region and having a similar intensity within that region as shown in IGV. However, bdgdiff still called out some narrow regions within the broad one in one of the conditions. I'm afraid that this kind of enriched peaks are not biologically meaningful as the histone enrichment is actually similar across the region. Is there any way to eliminate this kind of "false positive" differential enriched peaks? Thanks!!

enter image description here enter image description here enter image description here enter image description here

ADD COMMENTlink modified 4 months ago • written 4 months ago by chiefcat70

I am not an expert on this, but I attended a class taught by the author of MMDiff and it looked great for differential peak calling. Maybe worth a try? The paper is here, the software is a bioconductor package.

ADD REPLYlink written 4 months ago by Fabio Marroni1.6k

Hi Fabio, thanks for your suggestion. However, MMDiff seems specific for calling sharp peaks e.g. TF peaks as from a review (https://academic.oup.com/bib/article-lookup/doi/10.1093/bib/bbv110#supplementary-data) I've read. By the way, what kind of ChIP-seq. did you analyse using this software?

enter image description here

Enlarged

ADD REPLYlink modified 4 months ago • written 4 months ago by chiefcat70

I only played with the exercises they gave us in the class, which - if I well remember - were H3K4me3 data. It is possible that things stand as you say, this is beyond my knowledge, sorry.

ADD REPLYlink written 4 months ago by Fabio Marroni1.6k

Do you have replicates per condition ?

ADD REPLYlink written 4 months ago by geek_y8.2k

Hi geek, yes I've got biological replicates but they were pooled (probably during/ just before peak calling).

ADD REPLYlink written 4 months ago by chiefcat70

If you have replicates, DiffBind is a really useful R package that make differential peak calling pretty straightforward. I was really impressed with it. If you don't have replicates, MAnorm is also useful for directly comparing two samples. Both will derive a consensus peak set to normalize and compare signal at these peaks across the samples/conditions/treatments. Sounds like they may be worth a look in your case.

ADD REPLYlink written 4 months ago by jared.andrews07540
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: 490 users visited in the last hour