why doesn't chromap require a restriction enzyme option like HiC-Pro?

[Linhua-Sun]

Hello @haowenz: 1. I am wondering how chromap handel Hi-C without knowing the information of restriction enzyme? 2. I am testing chromap with a Hi-C library using combination of two restriction enzymes. And I have generated pairs files. Then can I convert .pairs into .hic or .cool files directly without any filter? Thanks！ Linhua

[haowenz]

1. Currently, Chromap doesn't check restriction enzyme motif at the clip sites. We plan to add this feature in the future.
2. You should at least dedup using pairtools, which can remove duplicates with both sides mapped to similar locations. Or when you run Chromap, you can add --remove-pcr-duplicates to the preset parameters and Chromap will only remove duplicates with both sides mapped to the same locations. You may also use other filters specific to your applications.

[Linhua-Sun]

Thanks for your quick reply. It solves well.