HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 04 2022
08 04 2022
Historique:
accepted:
04
12
2021
revised:
19
11
2021
received:
14
10
2020
pubmed:
21
12
2021
medline:
16
4
2022
entrez:
20
12
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 34928367
pii: 6470675
doi: 10.1093/nar/gkab1235
pmc: PMC8990515
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e35Subventions
Organisme : Intramural NIH HHS
ID : ZIA EY000546
Pays : United States
Organisme : Intramural NIH HHS
ID : ZIA EY000450
Pays : United States
Informations de copyright
Published by Oxford University Press on behalf of Nucleic Acids Research 2021.
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