MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads.
3′ end reads
Alternative polyadenylation
Bioinformatic tool
Cellular stress
RNA sequencing
Trophoblasts
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
10 08 2021
10 08 2021
Historique:
received:
03
02
2021
accepted:
01
07
2021
entrez:
11
8
2021
pubmed:
12
8
2021
medline:
20
1
2022
Statut:
epublish
Résumé
Most eukaryotic genes express alternative polyadenylation (APA) isoforms. A growing number of RNA sequencing methods, especially those used for single-cell transcriptome analysis, generate reads close to the polyadenylation site (PAS), termed nearSite reads, hence inherently containing information about APA isoform abundance. Here, we present a probabilistic model-based method named MAAPER to utilize nearSite reads for APA analysis. MAAPER predicts PASs with high accuracy and sensitivity and examines different types of APA events with robust statistics. We show MAAPER's performance with both bulk and single-cell data and its applicability in unpaired or paired experimental designs.
Identifiants
pubmed: 34376236
doi: 10.1186/s13059-021-02429-5
pii: 10.1186/s13059-021-02429-5
pmc: PMC8356463
doi:
Substances chimiques
3' Untranslated Regions
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
222Subventions
Organisme : NCI NIH HHS
ID : P30 CA010815
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM084089
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM129069
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR003017
Pays : United States
Informations de copyright
© 2021. The Author(s).
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