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!
1 answer
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.
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