I am wondering how HiC-Pro deals with chloroplast and mitochondrial DNA. I expect that eventually we might want to filter them out from our results.
Should I remove them from the input genome files (including chromosome sizes and bowtie2 indexes) or is HiC-Pro capable of ignoring them? I just want to be sure that they are not affecting anything in my pipeline.
Hi,
I am wondering how HiC-Pro deals with chloroplast and mitochondrial DNA. I expect that eventually we might want to filter them out from our results.
Should I remove them from the input genome files (including chromosome sizes and bowtie2 indexes) or is HiC-Pro capable of ignoring them? I just want to be sure that they are not affecting anything in my pipeline.
Thanks!