Duplicates in preset Hi-C mode about chromap HOT 6 CLOSED

Chromap does not remove PCR duplicates in Hi-C through the preset option. You can find the information at the bottom of the manual page here: https://zhanghaowen.com/chromap/chromap.html .

If you want to remove the duplicates, you can add the option "--remove-pcr-duplicates".

from chromap.

Chromap does not remove PCR duplicates in Hi-C through the preset option. You can find the information at the bottom of the manual page here: https://zhanghaowen.com/chromap/chromap.html .

If you want to remove the duplicates, you can add the option "--remove-pcr-duplicates".

Great, thank you so much!

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I just want to mention one of the main reasons that we did not add the PCR deduplication as the default behavior. The deduplication is based on alignment coordinates, and we did not keep track of the internal alignment breakpoint (ligation site) in Hi-C data. So if two read pairs have the same endpoints, but have different ligation sites, one of them will still be removed in the deduplication step.

from chromap.

I just want to mention one of the main reasons that we did not add the PCR deduplication as the default behavior. The deduplication is based on alignment coordinates, and we did not keep track of the internal alignment breakpoint (ligation site) in Hi-C data. So if two read pairs have the same endpoints, but have different ligation sites, one of them will still be removed in the deduplication step.

Thank you for your detailed explanation. That make senses. I just want to clarify that, only read pairs, of which both end reads are duplicated, will be considered as duplicates in chromap? Thanks!

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Just following up to see if we can get an answer for @jimwry's previous question? I'm working on integrating chromap with https://github.com/c-zhou/yahs. Thanks!

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Sorry I missed that question. To answer the question, yes, we only consider the endpoints in deduplication for read pairs in the pairs output format. For single-end read, it is only the start site on the reference genome.

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