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dc.contributor.author | Ruiz Reche, Angel |
dc.contributor.author | Srivastava, Akanksha |
dc.contributor.author | Indi, Joel A. |
dc.contributor.author | de la Rubia, Ivan |
dc.contributor.author | Eyras Jiménez, Eduardo |
dc.date.accessioned | 2020-06-17T06:47:31Z |
dc.date.available | 2020-06-17T06:47:31Z |
dc.date.issued | 2019 |
dc.identifier.citation | Ruiz-Reche A, Srivastava A, Indi JA, de la Rubia I, Eyras E. ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning. Genome Biol. 2019; 20(1):260. DOI: 10.1186/s13059-019-1884-z |
dc.identifier.issn | 1474-7596 |
dc.identifier.uri | http://hdl.handle.net/10230/44994 |
dc.description.abstract | We describe ReorientExpress, a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep learning to correctly predict the orientation of the majority of reads, and in particular when trained on a closely related species or in combination with read clustering. ReorientExpress enables long-read transcriptomics in non-model organisms and samples without a genome reference without using additional technologies and is available at https://github.com/comprna/reorientexpress. |
dc.description.sponsorship | Part of this work was funded by the Spanish Government and FEDER with grants BIO2017-85364-R and MDM-2014-0370 and by Catalan Government (AGAUR) with grant SGR2017-1020. JI was supported by a PhD grant from FCT (Fundação para a Ciência e a Tecnologia) Portugal. IdlR had funding from an FPI grant from the Spanish Government (PRE2018-083413). |
dc.format.mimetype | application/pdf |
dc.language.iso | eng |
dc.publisher | BioMed Central |
dc.relation.ispartof | Genome Biol. 2019; 20(1):260 |
dc.rights | © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ |
dc.title | ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning |
dc.type | info:eu-repo/semantics/article |
dc.identifier.doi | http://dx.doi.org/10.1186/s13059-019-1884-z |
dc.relation.projectID | info:eu-repo/grantAgreement/ES/2PE/BIO2017-85364-R |
dc.rights.accessRights | info:eu-repo/semantics/openAccess |
dc.type.version | info:eu-repo/semantics/publishedVersion |