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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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How to differ the loops we detect from exp and ctl? #854

Open wikk-chy opened 1 year ago

wikk-chy commented 1 year ago

Hi! Thank you for developing a great suite of tools, and for the excellent documentation.I have a question about calling loops and finding different loops.

I have used the commond hicDetectLoops getting loops file by experiment and control. And I want to find some difference between the two targets. However, I have tried the hiccupsdiff to solve the problem, there is no use which might be caused I can not detect loops by the hiccups. I do not know why I can detect loops by using hicDetectLoops on the .cool matrix corrected by KR rather than balance, and there is no way calling loops by hiccups.

Totally, I hope you could add a differloops function for hicexplore which can be used for hicDetectLoops result directly.

wikk-chy commented 1 year ago

I try to detect loops in 1k resolution, and my whole genome is around 4M.