HiCCUPS Diff allows you to find differential loops between loop lists.

Usage

hiccupsdiff [-m matrixSize] [-k normalization (NONE/VC/VC_SQRT/KR)] [-c chromosome(s)] [-f fdr] [-p peak width] [-i window] [-t thresholds] [-d centroid distances] <firstHicFile> <secondHicFile> <firstLoopList> <secondLoopList> <outputDirectory>

HiCCUPSDiff works by checking the loops called in each hic file on the other; it checks them by again calling HiCCUPS.

Required options

firstHicFile - first .hic file to compare secondHicFile - second .hic file to compare firstLoopList - first loop list, that is, the result (merged_loops) of running HiCCUPS on the first .hic file secondLoopList - second loop list, that is, the result (merged_loops) of running HiCCUPS on the second .hic file outputDirectory - output directory. Will contain differentialLoopList1, containing loops that appear in the first loop list and are not present in the second hic file, and differentialLoopList2, containing loops that appear in the second loop list and are not present in the first hic file

Optional options

This function takes optional HiCCUPS arguments; these are explained in the HiCCUPS section.