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

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...

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Detalles Bibliográficos
Autores: Trincado Alonso, Juan Luis, 1987-, Entizne, Juan Carlos, Hysenaj, Gerald, Singh, Babita, 1986-, Skalic, Miha, 1990-, Elliott, David, 1947-, Eyras Jiménez, Eduardo
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2018
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/34592
Acceso en línea:http://hdl.handle.net/10230/34592
http://dx.doi.org/10.1186/s13059-018-1417-1
Access Level:acceso abierto
Palabra clave:Differential splicing
Alternative splicing
RNA-seq
Biological variability
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spelling SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditionsTrincado Alonso, Juan Luis, 1987-Entizne, Juan CarlosHysenaj, GeraldSingh, Babita, 1986-Skalic, Miha, 1990-Elliott, David, 1947-Eyras Jiménez, EduardoDifferential splicingAlternative splicingRNA-seqBiological variabilityDespite 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.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.BioMed Central201820182018info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/34592http://dx.doi.org/10.1186/s13059-018-1417-1reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésGenome Biology. 2018 Dec;19(1):40info:eu-repo/grantAgreement/ES/1PE/BIO2014-52566-Rinfo:eu-repo/grantAgreement/ES/2PE/BIO2017-85364-R© 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.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/345922026-05-29T05:05:01Z
dc.title.none.fl_str_mv SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
title SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
spellingShingle SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
Trincado Alonso, Juan Luis, 1987-
Differential splicing
Alternative splicing
RNA-seq
Biological variability
title_short SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
title_full SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
title_fullStr SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
title_full_unstemmed SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
title_sort SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
dc.creator.none.fl_str_mv Trincado Alonso, Juan Luis, 1987-
Entizne, Juan Carlos
Hysenaj, Gerald
Singh, Babita, 1986-
Skalic, Miha, 1990-
Elliott, David, 1947-
Eyras Jiménez, Eduardo
author Trincado Alonso, Juan Luis, 1987-
author_facet Trincado Alonso, Juan Luis, 1987-
Entizne, Juan Carlos
Hysenaj, Gerald
Singh, Babita, 1986-
Skalic, Miha, 1990-
Elliott, David, 1947-
Eyras Jiménez, Eduardo
author_role author
author2 Entizne, Juan Carlos
Hysenaj, Gerald
Singh, Babita, 1986-
Skalic, Miha, 1990-
Elliott, David, 1947-
Eyras Jiménez, Eduardo
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Differential splicing
Alternative splicing
RNA-seq
Biological variability
topic Differential splicing
Alternative splicing
RNA-seq
Biological variability
description 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.
publishDate 2018
dc.date.none.fl_str_mv 2018
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/34592
http://dx.doi.org/10.1186/s13059-018-1417-1
url http://hdl.handle.net/10230/34592
http://dx.doi.org/10.1186/s13059-018-1417-1
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Genome Biology. 2018 Dec;19(1):40
info:eu-repo/grantAgreement/ES/1PE/BIO2014-52566-R
info:eu-repo/grantAgreement/ES/2PE/BIO2017-85364-R
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812429

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