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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.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.issn 2073-4425
dc.identifier.uri http://hdl.handle.net/10230/42350
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.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.uri http://creativecommons.org/licenses/by/4.0/
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.identifier.doi http://dx.doi.org/10.3390/genes10070548
dc.subject.keyword Hi-C
dc.subject.keyword Capture Hi-C
dc.subject.keyword Processing
dc.subject.keyword Quality control
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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