REPAC: analysis of alternative polyadenylation from RNA-sequencing data
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Feb 09, 2023
- Source ID
- 10.1186/s13059-023-02865-5
Entities
People
- Benjamin Langmead
- Christopher Wilks
- Eddie Luidy Imada
- Luigi Marchionni
Organizations
- Foundation for the National Institutes of Health