Algorithmic considerations when analysing capture Hi-C data.
Date
2020-01-01Author
Disney-Hogg, L
Kinnersley, B
Houlston, R
Type
Journal Article
Metadata
Show full item recordAbstract
Chromosome conformation capture methodologies have provided insight into the effect of 3D genomic architecture on gene regulation. Capture Hi-C (CHi-C) is a recent extension of Hi-C that improves the effective resolution of chromatin interactions by enriching for defined regions of biological relevance. The varying targeting efficiency between capture regions, however, introduces bias not present in conventional Hi-C, making analysis more complicated. Here we consider salient features of an algorithm that should be considered in evaluating the performance of a program used to analyse CHi-C data in order to infer meaningful interactions. We use the program CHICAGO to analyse promoter capture Hi-C data generated on 28 different cell lines as a case study.
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Research team
Cancer Genomics
Language
eng
Date accepted
2020-01-01
License start date
2020-01-01
Citation
Wellcome Open Research, 2020, 5 pp. 289 -