biostudies-literatureFreire-Pritchett PMedical Research CouncilWellcome TrustBiotechnology and Biological Sciences Research Council4144-4176https://www.ebi.ac.uk/biostudies/studies/S-EPMC7612634biostudies-literatureUnknown16(9)Capture Hi-C is widely used to obtain high-resolution profiles of chromosomal interactions involving, at least on one end, regions of interest such as gene promoters. Signal detection in Capture Hi-C data is challenging and cannot be adequately accomplished with tools developed for other chromosome conformation capture methods, including standard Hi-C. Capture Hi-C Analysis of Genomic Organization (CHiCAGO) is a computational pipeline developed specifically for Capture Hi-C analysis. It implements a statistical model accounting for biological and technical background components, as well as bespoke normalization and multiple testing procedures for this data type. Here we provide a step-by-step guide to the CHiCAGO workflow that is aimed at users with basic experience of the command line andNature protocolsDetecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.PMC7612634107881107881/Z/15/Z215097215097/Z/18/ZMC_UP_1605/3WT107881MC_UU_00002/4MC-A652-5QA20Wingett SWSpivakov MCairns JDella Rosa MMalysheva VFreire-Pritchett PWallace COrchard WRRay-Jones HEijsbouts CQfalseDetecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.Capture Hi-C is widely used to obtain high-resolution profiles of chromosomal interactions involving, at least on one end, regions of interest such as gene promoters. Signal detection in Capture Hi-C data is challenging and cannot be adequately accomplished with tools developed for other chromosome conformation capture methods, including standard Hi-C. Capture Hi-C Analysis of Genomic Organization (CHiCAGO) is a computational pipeline developed specifically for Capture Hi-C analysis. It implements a statistical model accounting for biological and technical background components, as well as bespoke normalization and multiple testing procedures for this data type. Here we provide a step-by-step guide to the CHiCAGO workflow that is aimed at users with basic experience of the command line and2021-01-01T00:00:00Z2021 Sep2025-04-04T08:52:46.468Z2025-04-04T08:52:46.468ZS-EPMC76126343437365210.1038/s41596-021-00567-5