Computational processing and quality control of Hi-C, capture Hi-C and capture-C data

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• dc.contributor.author Hansen, Peter
• dc.contributor.author Gargano, Michael
• dc.contributor.author Hecht, Jochen
• dc.contributor.author Ibn-Salem, Jonas
• dc.contributor.author Karlebach, Guy
• dc.contributor.author Roehr, Johannes T.
• dc.contributor.author Robinson, Peter N.
• dc.date.accessioned 2019-09-27T08:16:01Z
• dc.date.available 2019-09-27T08:16:01Z
• dc.date.issued 2019
• dc.description.abstract 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.
• dc.format.mimetype application/pdf
• dc.identifier.citation Hansen P, Gargano M, Hecht J, Ibn-Salem J, Karlebach G, Roehr JT, Robinson PN. Computational processing and quality control of Hi-C, capture Hi-C and capture-C data. Genes (Basel). 2019; 10(7). pii: E548. DOI 10.3390/genes10070548
• dc.identifier.doi http://dx.doi.org/10.3390/genes10070548
• dc.identifier.issn 2073-4425
• dc.identifier.uri http://hdl.handle.net/10230/42350
• dc.language.iso eng
• dc.publisher MDPI
• dc.relation.ispartof Genes (Basel). 2019; 10(7). pii: E548
• dc.rights © 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/).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Hi-C
• dc.subject.keyword Capture Hi-C
• dc.subject.keyword Processing
• dc.subject.keyword Quality control
• dc.title Computational processing and quality control of Hi-C, capture Hi-C and capture-C data
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion