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.