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Assessment of transcript reconstruction methods for RNA-seq

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dc.contributor.author Steijger, Tamara
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author RGASP Consortium
dc.date.accessioned 2015-02-05T08:37:29Z
dc.date.available 2015-02-05T08:37:29Z
dc.date.issued 2013
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.2714
dc.identifier.issn 1548-7091
dc.identifier.uri http://hdl.handle.net/10230/23096
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/pdf
dc.language.iso eng
dc.publisher Nature Publishing Group
dc.relation.ispartof Nature Methods. 2013;10(12):1177-84
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 License
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-seq
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1038/nmeth.2714
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-26205
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/CSD2007-00050
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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