Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data.
Hi-C
capture Hi-C
processing
quality control
Journal
Genes
ISSN: 2073-4425
Titre abrégé: Genes (Basel)
Pays: Switzerland
ID NLM: 101551097
Informations de publication
Date de publication:
18 07 2019
18 07 2019
Historique:
received:
15
05
2019
revised:
06
07
2019
accepted:
14
07
2019
entrez:
21
7
2019
pubmed:
22
7
2019
medline:
7
1
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 31323892
pii: genes10070548
doi: 10.3390/genes10070548
pmc: PMC6678864
pii:
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NCI NIH HHS
ID : P30 CA034196
Pays : United States
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