REPAC: analysis of alternative polyadenylation from RNA-sequencing data

被引：4

作者：

Imada, Eddie L. ^{[1
]}

Wilks, Christopher ^{[2
]}

Langmead, Ben ^{[2
]}

Marchionni, Luigi ^{[1
]}

机构：

[1] Weill Cornell Med, Dept Pathol, Lab Med, New York, NY 10021 USA

[2] Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD USA

来源：

GENOME BIOLOGY | 2023年 / 24卷 / 01期

基金：

美国国家科学基金会;

关键词：

Polyadenylation; Method; Compositions; ACTIVATION; CLEAVAGE; PTP1B;

D O I：

10.1186/s13059-023-02865-5

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：14

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