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

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• dc.contributor.author Trincado Alonso, Juan Luis, 1987-ca
• dc.contributor.author Entizne, Juan Carlosca
• dc.contributor.author Hysenaj, Geraldca
• dc.contributor.author Singh, Babita, 1986-ca
• dc.contributor.author Skalic, Miha, 1990-ca
• dc.contributor.author Elliott, David, 1947-ca
• dc.contributor.author Eyras Jiménez, Eduardoca
• dc.date.accessioned 2018-05-09T09:39:29Z
• dc.date.available 2018-05-09T09:39:29Z
• dc.date.issued 2018
• dc.description.abstract 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.
• dc.description.sponsorship This work was supported by the MINECO and FEDER with grants BIO2014-52566-R and BIO2017-85364-R, by AGAUR with grants SGR2014-1121 and SGR2017-1020, by BBSRC (BB/P006612/1), and by Breast Cancer Now (2014NovPR355). GH is a BBSRC-funded PhD student.
• dc.format.mimetype application/pdf
• dc.identifier.citation Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ et al. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol. 2018 Dec;19(1):40. DOI: 10.1186/s13059-018-1417-1
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-018-1417-1
• dc.identifier.issn 1474-7596
• dc.identifier.uri http://hdl.handle.net/10230/34592
• dc.language.iso eng
• dc.publisher BioMed Centralca
• dc.relation.ispartof Genome Biology. 2018 Dec;19(1):40
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2014-52566-R
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BIO2017-85364-R
• dc.rights © The Author(s). 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Differential splicing
• dc.subject.keyword Alternative splicing
• dc.subject.keyword RNA-seq
• dc.subject.keyword Biological variability
• dc.title SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditionsca
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion