Related Experiment Video
Updated: Mar 26, 2026
Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
Published on: October 14, 2022
HiCUP: pipeline for mapping and processing Hi-C data
Steven Wingett1, Philip Ewels2, Mayra Furlan-Magaril3
1Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK; Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
Abstract:
HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also produces an easy-to-interpret yet detailed quality control (QC) report that assists in refining experimental protocols for future studies. The software is freely available and has already been used for processing Hi-C and CHi-C data in several recently published peer-reviewed studies.
