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cvlr: finding heterogeneously methylated genomic regions using ONT reads

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dc.contributor.author Raineri, Emanuele
dc.contributor.author Alberola i Pla, Mariona
dc.contributor.author Dabad, Marc
dc.contributor.author Heath, Simon
dc.date.accessioned 2023-06-20T06:24:38Z
dc.date.available 2023-06-20T06:24:38Z
dc.date.issued 2023
dc.identifier.citation Raineri E, Alberola I Pla M, Dabad M, Heath S. cvlr: finding heterogeneously methylated genomic regions using ONT reads. Bioinform Adv. 2023 Jan 23;3(1):vbac101. DOI: 10.1093/bioadv/vbac101
dc.identifier.issn 2635-0041
dc.identifier.uri http://hdl.handle.net/10230/57257
dc.description.abstract Summary: Nanopore reads encode information on the methylation status of cytosines in CpG dinucleotides. The length of the reads makes it comparatively easy to look at patterns consisting of multiple loci; here, we exploit this property to search for regions where one can define subpopulations of molecules based on methylation patterns. As an example, we run our clustering algorithm on known imprinted genes; we also scan chromosome 15 looking for windows corresponding to heterogeneous methylation. Our software can also compute the covariance of methylation across these regions while keeping into account the mixture of different types of reads. Availability and implementation: https://github.com/EmanueleRaineri/cvlr. Contact: simon.heath@cnag.crg.eu. Supplementary information: Supplementary data are available at Bioinformatics Advances online.
dc.description.sponsorship This work was supported by a Spanish Plan Nacional grant [project: PGC2018-099640-B-I00]. Furthermore, we acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, of the Centro de Excelencia Severo Ochoa and of the CERCA Programme/Generalitat de Catalunya. We also acknowledge support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III of the Generalitat de Catalunya through Departament de Salut and Departament d’Universitats i Recerca. We also acknowledge the Co-financing with funds from the European Regional Development Fund by the Spanish Ministry of Science and Innovation corresponding to the Programa Operativo FEDER Plurirregional de España (POPE) 2014–2020 and by the Departament d’Universitats i Recerca of the Generalitat de Catalunya corresponding to the Programa Operatiu FEDER de Catalunya 2014–2020.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Bioinform Adv. 2023 Jan 23;3(1):vbac101
dc.rights © The Author(s) 2023. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title cvlr: finding heterogeneously methylated genomic regions using ONT reads
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/bioadv/vbac101
dc.subject.keyword Genome analysis
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-099640-B-I00
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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