HiCUP: pipeline for mapping and processing Hi-C data.
Published version
Peer-reviewed
Repository URI
Repository DOI
Change log
Authors
Wingett, Steven
Ewels, Philip
Furlan-Magaril, Mayra
Nagano, Takashi
Schoenfelder, Stefan https://orcid.org/0000-0002-3200-8133
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.
Description
Keywords
Bioinformatics, CHi-C, Chromatin, Epigenetics, Genomics, Hi-C, Pipeline, Structure
Journal Title
F1000Res
Conference Name
Journal ISSN
2046-1402
1759-796X
1759-796X
Volume Title
4
Publisher
F1000 Research Ltd
Publisher DOI
Sponsorship
Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0405)
Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0404)
Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0404)