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Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data
Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensiona...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678864/ https://www.ncbi.nlm.nih.gov/pubmed/31323892 http://dx.doi.org/10.3390/genes10070548 |
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author | Hansen, Peter Gargano, Michael Hecht, Jochen Ibn-Salem, Jonas Karlebach, Guy Roehr, Johannes T. Robinson, Peter N. |
author_facet | Hansen, Peter Gargano, Michael Hecht, Jochen Ibn-Salem, Jonas Karlebach, Guy Roehr, Johannes T. Robinson, Peter N. |
author_sort | Hansen, Peter |
collection | PubMed |
description | Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish technical artefacts from valid read pairs originating from true chromatin interactions. |
format | Online Article Text |
id | pubmed-6678864 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-66788642019-08-19 Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data Hansen, Peter Gargano, Michael Hecht, Jochen Ibn-Salem, Jonas Karlebach, Guy Roehr, Johannes T. Robinson, Peter N. Genes (Basel) Review Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish technical artefacts from valid read pairs originating from true chromatin interactions. MDPI 2019-07-18 /pmc/articles/PMC6678864/ /pubmed/31323892 http://dx.doi.org/10.3390/genes10070548 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Review Hansen, Peter Gargano, Michael Hecht, Jochen Ibn-Salem, Jonas Karlebach, Guy Roehr, Johannes T. Robinson, Peter N. Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data |
title | Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data |
title_full | Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data |
title_fullStr | Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data |
title_full_unstemmed | Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data |
title_short | Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data |
title_sort | computational processing and quality control of hi-c, capture hi-c and capture-c data |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678864/ https://www.ncbi.nlm.nih.gov/pubmed/31323892 http://dx.doi.org/10.3390/genes10070548 |
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