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SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Lookup NU author(s): Gerald Hysenaj, Professor David Elliott

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© 2018 The Author(s). Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data, we show that SUPPA2 achieves higher accuracy compared to other methods, especially at low sequencing depth and short read length. We use SUPPA2 to identify novel Transformer2-regulated exons, novel microexons induced during differentiation of bipolar neurons, and novel intron retention events during erythroblast differentiation.

Publication metadata

Author(s): Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ, Eyras E

Publication type: Article

Publication status: Published

Journal: Genome Biology

Year: 2018

Volume: 19

Issue: 1

Pages: 40

Online publication date: 23/03/2018

Acceptance date: 02/03/2018

Date deposited: 10/04/2018

ISSN (print): 1474-7596

ISSN (electronic): 1474-760X

Publisher: BioMed Central Ltd.

URL: https://doi.org/10.1186/s13059-018-1417-1

DOI: 10.1186/s13059-018-1417-1

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