ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning

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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.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.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.doi http://dx.doi.org/10.1186/s13059-019-1884-z
  • dc.identifier.issn 1474-7596
  • dc.identifier.uri http://hdl.handle.net/10230/44994
  • dc.language.iso eng
  • dc.publisher BioMed Central
  • dc.relation.ispartof Genome Biol. 2019; 20(1):260
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BIO2017-85364-R
  • 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.accessRights info:eu-repo/semantics/openAccess
  • 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.type.version info:eu-repo/semantics/publishedVersion

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