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Systematic evaluation of spliced alignment programs for RNA-seq data

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dc.contributor.author Engström, Pär G.
dc.contributor.author Steijger, Tamara
dc.contributor.author Sipos, Botond
dc.contributor.author Grant, Gregory R.
dc.contributor.author Kahles, André
dc.contributor.author RGASP Consortium
dc.contributor.author Rätsch, Gunnar
dc.contributor.author Goldman, Nick
dc.contributor.author Hubbard, Tim J.
dc.contributor.author Harrow, Jennifer
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Bertone, Paul
dc.date.accessioned 2015-12-02T17:38:43Z
dc.date.available 2015-12-02T17:38:43Z
dc.date.issued 2013
dc.identifier.citation Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G et al. Systematic evaluation of spliced alignment programs for RNA-seq data. Nature methods. 2013;10(12):1185-91. DOI: 10.1038/nmeth.2722
dc.identifier.issn 1548-7091
dc.identifier.uri http://hdl.handle.net/10230/25316
dc.description.abstract High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Nature Publishing Group
dc.relation.ispartof Nature methods. 2013;10(12):1185-91
dc.relation.ispartof Nature methods. 2013;10(12):1185-91
dc.rights © 2013 Nature America, Inc. All rights reserved. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/
dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/3.0/
dc.subject.other Gens Mapatge
dc.subject.other Empalmament (Genètica)
dc.title Systematic evaluation of spliced alignment programs for RNA-seq data
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1038/nmeth.2722
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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