Will mitochondria DNA affect the sequencing in ATAC-seq?

Question

[ghostforever.shi]

Hello everyone, I have a question about the mtDNA in ATAC-seq.

As is known, abundant mitochondrial DNA (mtDNA) will be found in sequencing libraries when doing ATAC-seq in some specific cell types (like ES cells). In fact, there are some ways to reduce the mitochondrial DNA, like using CRISPR/Cas9. My question is, whether the procedure of removing the mitochondrial DNA is necessary (except for the reason of higher cost on sequencing to generate more useful reads since the high proportion of mtDNA in sequencing libraries may decrease the number of reads needed for analysis.) and will the existence of mtDNA generate some sequencing bias (like GC bias or something else)?

Thank you.

Answer 1

[ATpoint]

I never read anything about sequencing problems related to chrM GC content, which is 44% for humans. The currently most effective and also simplest strategy to avoid chrM contamination is the use of the OmniATAC protocol. I would always make use of it, as it dramatically increases the number of usable reads. Still, given that you simply sequenced the heck out of your libraries, removal is not crucial and could be compensated by very deep sequencing, but this would be absolutely uneconomic, especially when you have multiple samples.