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merge_filter reduces significant interactions from 12M to 10k #57

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pna059 opened this issue Jul 25, 2022 · 0 comments
Open

merge_filter reduces significant interactions from 12M to 10k #57

pna059 opened this issue Jul 25, 2022 · 0 comments

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@pna059
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pna059 commented Jul 25, 2022

I am using HiC-Pro/FitHiC tools for calling interactions from two Hi-C replicates for a large genome. FitHiC2 at 20kb resolution (40kb-2Mb) found 12M interactions with q-value <0.005 (from ".spline_pass2.res20000.significances.txt.gz" file). After running the default merge_filter.sh, the number went down to 10kb with FDR=0.05. Is this normal or is it possible that I need to adjust some parameters in CombineNearbyInteraction.py? I could not find details on this step.
Thank you for the great toolkits and help!
Pavla
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