Document Type
Article
Publication Date
7-18-2019
Keywords
JGM
JAX Source
Genes (Basel) 2019 Jul 18; 10(7):E548
Volume
10
Issue
7
ISSN
2073-4425
PMID
31323892
DOI
https://doi.org/10.3390/genes10070548
Grant
CA034196,Agilent Rhought Leader Award, Donald A. Roux family fund
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.
Recommended Citation
Hansen P,
Gargano M,
Hecht J,
Ibn-Salem J,
Karlebach G,
Roehr J,
Robinson P.
Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data. Genes (Basel) 2019 Jul 18; 10(7):E548
Comments
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/).