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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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Zero loops? #676

Closed gdolsten closed 3 years ago

gdolsten commented 3 years ago

Hi, for some reason HiCExplorer returns zero loops. I am currently running the following code: hicDetectLoops -m data_800.cool -o 400_loops.bedgraph -tpc 16 --windowSize 10 --peakWidth 6 Where the data is at 800bp resolution. Do you know what might be causing this issue?

joachimwolff commented 3 years ago

HI,

800 bp? That is really high. Are you sure your read coverage is high enough? I developed the loop detection with 10 kb data.

Can you plot a small region with hicPlotMatrix where there has to be a loop to validate there is any? Moreover, what is the scientific goal you try to achieve? Enhancer-Promoter interactions? Best,

Joachim

joachimwolff commented 3 years ago

No user response. Closing.