Assessment of transcript reconstruction methods for RNA-seq
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- dc.contributor.author Steijger, Tamaraca
- dc.contributor.author Guigó Serra, Rodericca
- dc.contributor.author RGASP Consortiumca
- dc.date.accessioned 2015-02-05T08:37:29Z
- dc.date.available 2015-02-05T08:37:29Z
- dc.date.issued 2013ca
- dc.description.abstract We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.
- dc.description.sponsorship This work was supported by grants BIO2011-26205 and CSD2007-00050 from the Ministerio de Educación y Ciencia
- dc.format.mimetype application/pdfca
- dc.identifier.citation Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R et al. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods. 2013;10(12):1177-84. DOI: 10.1038/nmeth.2714ca
- dc.identifier.doi http://dx.doi.org/10.1038/nmeth.2714
- dc.identifier.issn 1548-7091ca
- dc.identifier.uri http://hdl.handle.net/10230/23096
- dc.language.iso engca
- dc.publisher Nature Publishing Groupca
- dc.relation.ispartof Nature Methods. 2013;10(12):1177-84
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-26205
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/CSD2007-00050
- dc.rights http://dx.doi.org/10.1038/nmeth.2714. This article is distributed under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licenseca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/3.0/
- dc.subject.other Biologia computacional
- dc.subject.other Empalmament (Genètica)
- dc.title Assessment of transcript reconstruction methods for RNA-seqca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca