Publicação
ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning
| 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, Eduardo | |
| dc.date.accessioned | 2022-04-13T15:36:10Z | |
| dc.date.available | 2022-04-13T15:36:10Z | |
| dc.date.issued | 2019 | |
| dc.description | © 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. | pt_PT |
| 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 | pt_PT |
| 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). | pt_PT |
| dc.description.version | info:eu-repo/semantics/publishedVersion | pt_PT |
| dc.identifier.citation | Genome Biol. 2019 Nov 29;20(1):260 | pt_PT |
| dc.identifier.doi | 10.1186/s13059-019-1884-z | pt_PT |
| dc.identifier.eissn | 1465-6906 | |
| dc.identifier.issn | 1474-760X | |
| dc.identifier.uri | http://hdl.handle.net/10451/52338 | |
| dc.language.iso | eng | pt_PT |
| dc.peerreviewed | yes | pt_PT |
| dc.publisher | Springer Nature | pt_PT |
| dc.relation.publisherversion | https://genomebiology.biomedcentral.com/ | pt_PT |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | pt_PT |
| dc.title | ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning | pt_PT |
| dc.type | journal article | |
| dspace.entity.type | Publication | |
| oaire.citation.issue | 1 | pt_PT |
| oaire.citation.title | Genome Biology | pt_PT |
| oaire.citation.volume | 20 | pt_PT |
| rcaap.rights | openAccess | pt_PT |
| rcaap.type | article | pt_PT |
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