REPAC: analysis of alternative polyadenylation from RNA-sequencing data.
Compositions
Method
Polyadenylation
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
09 02 2023
09 02 2023
Historique:
received:
30
03
2022
accepted:
24
01
2023
entrez:
10
2
2023
pubmed:
11
2
2023
medline:
14
2
2023
Statut:
epublish
Résumé
Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, availability of these data are limited compared to RNA-sequencing data. We developed REPAC, a framework for the analysis of APA from RNA-sequencing data. Using REPAC, we investigate the landscape of APA caused by activation of B cells. We also show that REPAC is faster than alternative methods by at least 7-fold and that it scales well to hundreds of samples. Overall, the REPAC method offers an accurate, easy, and convenient solution for the exploration of APA.
Identifiants
pubmed: 36759904
doi: 10.1186/s13059-023-02865-5
pii: 10.1186/s13059-023-02865-5
pmc: PMC9912678
doi:
Substances chimiques
3' Untranslated Regions
0
RNA, Messenger
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
22Subventions
Organisme : NCI NIH HHS
ID : R01 CA200859
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM121459
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM139602
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA211024
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM118568
Pays : United States
Informations de copyright
© 2023. The Author(s).
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