Computational processing and quality control of Hi-C, capture Hi-C and capture-C data
| Autor: | Johannes T. Roehr, Peter N. Robinson, Peter Hansen, Michael A. Gargano, Guy Karlebach, Jonas Ibn-Salem, Jochen Hecht |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
lcsh:QH426-470 media_common.quotation_subject Context (language use) Review Computational biology Biology Processing Genome Capture Hi-C 03 medical and health sciences 0302 clinical medicine Hi-C Databases Genetic Genetics Transcriptional regulation Humans Quality (business) Enhancer Control (linguistics) Genetics (clinical) media_common Chromosome Mapping Computational Biology High-Throughput Nucleotide Sequencing Quality control Genomics Chromatin lcsh:Genetics 030104 developmental biology 030220 oncology & carcinogenesis |
| Zdroj: | Genes, Vol 10, Iss 7, p 548 (2019) Genes |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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