REPAC: analysis of alternative polyadenylation from RNA-sequencing data

Eddie L. Imada, Christopher Wilks, Ben Langmead, Luigi Marchionni

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article number22
JournalGenome biology
Volume24
Issue number1
DOIs
StatePublished - Dec 2023
Externally publishedYes

Keywords

  • Compositions
  • Method
  • Polyadenylation

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Cell Biology

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