joachimwolff
commented
2 years ago It's a file containing the information where proteins are located, for example ChIP-Seq CTCF data. https://raw.githubusercontent.com/deeptools/HiCExplorer/master/hicexplorer/test/test_data/hicHyperoptDetectLoops/ctcf_sorted.bed However, to just detect loops please use hicDetectLoops. The tool you listed is only for parameter optimisation of hicDetectLoops: https://hicexplorer.readthedocs.io/en/latest/content/tools/hicDetectLoops.html#hicdetectloops
Hello! I want use the 'hicHyperoptDetectLoops' command to call loops ,but I don't know what is '--proteinFile'. Can you give me a example? Thanks for your help.