I would like to extract the not chimeric reads from hic data and create a bam file with it. I have been trying, but with not much success. I saw that maybe with DiffHic could be feasible (currently checking) or with HiCPro that generates a sam file with the chimeric reads (I need to know how to subtract this from the original sam/bam file).
So, I would like to know if some of you have ideas or suggestions.
Thanks a lot!