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.
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页数：14
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