title: HiCUP: pipeline for mapping and processing Hi-C data.
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.
authors.affiliation: Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK; Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
authors.forename: Steven
authors.initials: S
authors.lastname: Wingett
authors.affiliation: Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
authors.forename: Philip
authors.initials: P
authors.lastname: Ewels
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
authors.forename: Mayra
authors.initials: M
authors.lastname: Furlan-Magaril
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
authors.forename: Takashi
authors.initials: T
authors.lastname: Nagano
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schoenfelder
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Fraser
authors.affiliation: Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: Andrews
keywords: Bioinformatics; CHi-C; Chromatin; Epigenetics; Genomics; Hi-C; Pipeline; Structure
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