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

Authors
  • Marchal, Claire1, 2
  • Singh, Nivedita1
  • Corso-Díaz, Ximena1
  • Swaroop, Anand1
  • 1 Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA.
  • 2 In silichrom Ltd, First Floor, Angel Court, 81 St Clements St, Oxford OX4 1AW, UK.
Type
Published Article
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Publication Date
Apr 08, 2022
Volume
50
Issue
6
Identifiers
DOI: 10.1093/nar/gkab1235
PMID: 34928367
Source
Medline
Language
English
License
Unknown

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. Published by Oxford University Press on behalf of Nucleic Acids Research 2021.

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