Compute with a protein peak data file (bed format) optimal parameters for the loop calling. Useful proteins are e.g. CTCF or cohesin.
A command line example is available below (easily matchable in Galaxy using each field information):
̀`$ hicHyperoptDetectLoops -m matrix.cool -o hyperopt_result.txt --maximumNumberOfLoops 10000 --resolution 10000 --runs 100`
For more information about HiCExplorer please consider our documentation on readthedocs.io.