6533b85ffe1ef96bd12c2795

RESEARCH PRODUCT

Computational processing and quality control of Hi-C, capture Hi-C and capture-C data

Johannes T. RoehrPeter N. RobinsonPeter HansenMichael A. GarganoGuy KarlebachJonas Ibn-salemJochen Hecht

subject

0301 basic medicine570lcsh:QH426-470media_common.quotation_subjectContext (language use)ReviewComputational biologyBiologyProcessingGenome576Capture Hi-C03 medical and health sciences0302 clinical medicineHi-CDatabases GeneticGeneticsTranscriptional regulationHumansQuality (business)EnhancerControl (linguistics)Genetics (clinical)media_commonGenomeChromosome MappingComputational BiologyHigh-Throughput Nucleotide SequencingQuality controlGenomicsChromatin004Chromatinlcsh:Genetics030104 developmental biology030220 oncology & carcinogenesis

description

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.

yearjournalcountryeditionlanguage
2019-01-01
10.3390/genes10070548http://hdl.handle.net/10230/42350