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

HiCUP: pipeline for mapping and processing Hi-C data.

Author information

1
Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK; Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
2
Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
3
Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
4
Bioinformatics Group, 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.

KEYWORDS:

Bioinformatics; CHi-C; Chromatin; Epigenetics; Genomics; Hi-C; Pipeline; Structure

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