Algorithmic considerations when analysing capture Hi-C data.
Loading...
Embargo End Date
ICR Authors
Authors
Disney-Hogg, L
Kinnersley, B
Houlston, R
Kinnersley, B
Houlston, R
Document Type
Journal Article
Date
2020-01-01
Date Accepted
2020-01-01
Abstract
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.
Citation
Wellcome Open Research, 2020, 5 pp. 289 -
Source Title
Wellcome Open Research
Publisher
ISSN
2398-502X
eISSN
2398-502X
2398-502X
2398-502X
Collections
Research Team
Cancer Genomics