Systematic evaluation of spliced alignment programs for RNA-seq data
Mostra el registre complet Registre parcial de l'ítem
- dc.contributor.author Engström, Pär G.ca
- dc.contributor.author Steijger, Tamaraca
- dc.contributor.author Sipos, Botondca
- dc.contributor.author Grant, Gregory R.ca
- dc.contributor.author Kahles, Andréca
- dc.contributor.author RGASP Consortiumca
- dc.contributor.author Rätsch, Gunnarca
- dc.contributor.author Goldman, Nickca
- dc.contributor.author Hubbard, Tim J.ca
- dc.contributor.author Harrow, Jenniferca
- dc.contributor.author Guigó Serra, Rodericca
- dc.contributor.author Bertone, Paulca
- dc.date.accessioned 2015-12-02T17:38:43Z
- dc.date.available 2015-12-02T17:38:43Z
- dc.date.issued 2013
- 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.ca
- dc.format.mimetype application/pdfca
- 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.2722ca
- dc.identifier.doi http://dx.doi.org/10.1038/nmeth.2722
- dc.identifier.issn 1548-7091
- dc.identifier.uri http://hdl.handle.net/10230/25316
- dc.language.iso engca
- dc.publisher Nature Publishing Groupca
- 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/ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/3.0/ca
- dc.subject.other Gens Mapatgeca
- dc.subject.other Empalmament (Genètica)ca
- dc.title Systematic evaluation of spliced alignment programs for RNA-seq dataca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca