HiCUP: pipeline for mapping and processing Hi-C data

F1000Res. 2015 Nov 20;4:1310. doi: 10.12688/f1000research.7334.1. eCollection 2015.


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.

Keywords: Bioinformatics; CHi-C; Chromatin; Epigenetics; Genomics; Hi-C; Pipeline; Structure.

Grant support

Research supported by the Medical Research Council and the Biotechnology and Biological Sciences Research Council of the UK.