Mitochondrial Genome In Chip-Seq?

Question

[Ian]

Do people include the mitochondrial genome (chrM) in ChIP-seq analyses? At the mapping and peak calling stages.

Answer 1

[User 59]

Well if you're not expecting to pull down chrM sequences, they could well be used as as good measure of background noise (due to the experimental procedure, rather than non-specific binding of whatever TF you have used). This paper might be of interest to you as it specifically discusses the contribution of chrM mapped sequences on a publicly available ChIP-Seq experiment.