dc.contributor.author | Gatto, Alberto | |
dc.contributor.author | Torroja, Carlos | |
dc.contributor.author | Mazzarotto, Francesco | |
dc.contributor.author | Cook, Stuart A | |
dc.contributor.author | Barton, Paul J R | |
dc.contributor.author | Sanchez-Cabo, Fatima | |
dc.contributor.author | Lara-Pezzi, Enrique | |
dc.date.accessioned | 2019-04-29T10:17:03Z | |
dc.date.available | 2019-04-29T10:17:03Z | |
dc.date.issued | 2014-04 | |
dc.identifier.citation | Nucleic Acids Res. 2014; 42(8):e71 | es_ES |
dc.identifier.issn | 1362-4962 | es_ES |
dc.identifier.uri | http://hdl.handle.net/20.500.12105/7528 | |
dc.description.abstract | Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon-exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/. | es_ES |
dc.description.sponsorship | European Union’s FP7 [ERG-239158 to E.L.-P., CardioNeT-ITN-289600 to E.L.-P., S.A.C. and P.J.R.B.]; Spanish Ministry of Science and Innovation [BFU2009-10016, SAF2012-31451 to E.L.-P.]; Regional Government of Madrid [2010-BMD-2321 ‘Fibroteam’ to E.L.-P.]; Spanish Ministry of Economy and Competitiveness and by the Pro-CNIC Foundation (towards CNIC); National Institute for Health Research Cardiovascular BRU at the Royal Brompton & Harefield NHS Foundation Trust and Imperial College London (to S.A.C. and P.J.B.). Funding for open access charge: European Union’s FP7 [ERG-239158, CardioNeT-ITN289600 to E.L.-P.] | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | Oxford University Press | es_ES |
dc.type.hasVersion | VoR | es_ES |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.subject.mesh | Algorithms | es_ES |
dc.subject.mesh | Sequence Alignment | es_ES |
dc.subject.mesh | Sequence Analysis, RNA | es_ES |
dc.subject.mesh | Software | es_ES |
dc.subject.mesh | Alternative Splicing | es_ES |
dc.subject.mesh | RNA Splice Sites | es_ES |
dc.title | FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions | es_ES |
dc.type | journal article | es_ES |
dc.rights.license | Atribución 4.0 Internacional | * |
dc.identifier.pubmedID | 24574529 | es_ES |
dc.format.volume | 42 | es_ES |
dc.format.number | 8 | es_ES |
dc.format.page | e71 | es_ES |
dc.identifier.doi | 10.1093/nar/gku166 | es_ES |
dc.contributor.funder | Unión Europea. Comisión Europea | |
dc.contributor.funder | Unión Europea. Comisión Europea. European Research Council (ERC) | |
dc.contributor.funder | Ministerio de Ciencia e Innovación (España) | |
dc.contributor.funder | Comunidad de Madrid (España) | |
dc.contributor.funder | Ministerio de Economía y Competitividad (España) | |
dc.contributor.funder | Fundación ProCNIC | |
dc.contributor.funder | National Health Service (Reino Unido) | |
dc.description.peerreviewed | Sí | es_ES |
dc.identifier.e-issn | 1362-4962 | es_ES |
dc.relation.publisherversion | https://doi.org/10.1093/nar/gku166 | es_ES |
dc.identifier.journal | Nucleic acids research | es_ES |
dc.repisalud.orgCNIC | CNIC::Grupos de investigación::Regulación Molecular de la Insuficiencia Cardiaca | es_ES |
dc.repisalud.orgCNIC | CNIC::Unidades técnicas::Bioinformática | es_ES |
dc.repisalud.institucion | CNIC | es_ES |
dc.relation.projectID | info:eu-repo/grantAgreement/EC/FP7/239158/EU | es_ES |
dc.relation.projectID | info:eu-repo/grantAgreement/EC/FP7/289600/EU | es_ES |
dc.relation.projectID | info:eu-repo/grantAgreement/ES/BFU2009-10016 | es_ES |
dc.relation.projectID | info:eu-repo/grantAgreement/ES/SAF2012-31451 | es_ES |
dc.rights.accessRights | open access | es_ES |