Extremely high ChIP-seq peak at mouse Chr2 "Gm10800" region

Question

[Ri]

I was dealing with some CUT&TAG ChIP-seq data(for TF).

After mapping and peak calling, I tried to use IGV to observe their peak distribution around the genome, and I found there are a a great number of peak/reads mapped to a specific region of chr2.

In gencode.vM21.primary_assembly.annotation.gtf, this region is described as "Gm10800".

I didn't found a lot information about Gm10800, so wondering if it's resonable and why?

Thanks in advance!

Answer 1

[ATpoint]

It overlaps a known artifact region that is prone to constantly accumulate excessive reads in NGS experiments. You can get blacklists for various genomes from https://github.com/Boyle-Lab/Blacklist/tree/master/lists which is based on this paper (https://www.nature.com/articles/s41598-019-45839-z). I always remove any peaks overlapping the blacklist in my preprocessing pipeline to remove these artifact regions from my peaksets.