HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries

Abstract Three-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. Hi-C is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a lib...

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Published inNucleic acids research Vol. 50; no. 6; p. e35
Main Authors Marchal, Claire, Singh, Nivedita, Corso-Díaz, Ximena, Swaroop, Anand
Format Journal Article
LanguageEnglish
Published England Oxford University Press 08.04.2022
Subjects
Chromatin - genetics
Chromosomes
Computational Biology - methods
Gene Library
Genome
Genomics
Methods Online
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Summary:Abstract Three-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. Hi-C is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a library is an essential step in any Hi-C experimental design. Here, we present the mathematical concepts to estimate the resolution of a dataset and predict whether deeper sequencing would enhance the resolution. We have developed HiCRes, a docker pipeline, by applying these concepts to several Hi-C libraries.
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkab1235