HiCUP: pipeline for mapping and processing Hi-C data

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 subsequen...

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Detalles Bibliográficos
Autores principales: Wingett, Steven, Ewels, Philip, Furlan-Magaril, Mayra, Nagano, Takashi, Schoenfelder, Stefan, Fraser, Peter, Andrews, Simon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2015
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706059/
https://www.ncbi.nlm.nih.gov/pubmed/26835000
http://dx.doi.org/10.12688/f1000research.7334.1
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author Wingett, Steven
Ewels, Philip
Furlan-Magaril, Mayra
Nagano, Takashi
Schoenfelder, Stefan
Fraser, Peter
Andrews, Simon
author_facet Wingett, Steven
Ewels, Philip
Furlan-Magaril, Mayra
Nagano, Takashi
Schoenfelder, Stefan
Fraser, Peter
Andrews, Simon
author_sort Wingett, Steven
collection PubMed
description 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.
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spelling pubmed-47060592016-01-29 HiCUP: pipeline for mapping and processing Hi-C data Wingett, Steven Ewels, Philip Furlan-Magaril, Mayra Nagano, Takashi Schoenfelder, Stefan Fraser, Peter Andrews, Simon F1000Res Software Tool Article 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. F1000Research 2015-11-20 /pmc/articles/PMC4706059/ /pubmed/26835000 http://dx.doi.org/10.12688/f1000research.7334.1 Text en Copyright: © 2015 Wingett S et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Wingett, Steven
Ewels, Philip
Furlan-Magaril, Mayra
Nagano, Takashi
Schoenfelder, Stefan
Fraser, Peter
Andrews, Simon
HiCUP: pipeline for mapping and processing Hi-C data
title HiCUP: pipeline for mapping and processing Hi-C data
title_full HiCUP: pipeline for mapping and processing Hi-C data
title_fullStr HiCUP: pipeline for mapping and processing Hi-C data
title_full_unstemmed HiCUP: pipeline for mapping and processing Hi-C data
title_short HiCUP: pipeline for mapping and processing Hi-C data
title_sort hicup: pipeline for mapping and processing hi-c data
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706059/
https://www.ncbi.nlm.nih.gov/pubmed/26835000
http://dx.doi.org/10.12688/f1000research.7334.1
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