Nanopore direct RNA sequencing data processing and analysis using MasterOfPores
Mostra el registre complet Registre parcial de l'ítem
- dc.contributor.author Cozzuto, Luca
- dc.contributor.author Delgado-Tejedor, Anna
- dc.contributor.author Hermoso Pulido, Antonio
- dc.contributor.author Novoa, Eva Maria
- dc.contributor.author Ponomarenko, Julia
- dc.date.accessioned 2025-04-03T12:40:01Z
- dc.date.available 2025-04-03T12:40:01Z
- dc.date.issued 2023
- dc.description.abstract This chapter describes MasterOfPores v.2 (MoP2), an open-source suite of pipelines for processing and analyzing direct RNA Oxford Nanopore sequencing data. The MoP2 relies on the Nextflow DSL2 framework and Linux containers, thus enabling reproducible data analysis in transcriptomic and epitranscriptomic studies. We introduce the key concepts of MoP2 and provide a step-by-step fully reproducible and complete example of how to use the workflow for the analysis of S. cerevisiae total RNA samples sequenced using MinION flowcells. The workflow starts with the pre-processing of raw FAST5 files, which includes basecalling, read quality control, demultiplexing, filtering, mapping, estimation of per-gene/transcript abundances, and transcriptome assembly, with support of the GPU computing for the basecalling and read demultiplexing steps. The secondary analyses of the workflow focus on the estimation of RNA poly(A) tail lengths and the identification of RNA modifications. The MoP2 code is available at https://github.com/biocorecrg/MOP2 and is distributed under the MIT license.
- dc.description.sponsorship This work was partly supported by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) (PGC2018-098152-A-100 to EMN). AD-T is supported by a Severo Ochoa FPI PhD fellowship from the MEIC (PRE2019-088498). We acknowledge the support of the MEIC to the EMBL partnership, Centro de Excelencia Severo Ochoa and CERCA Programme/Generalitat de Catalunya.
- dc.format.mimetype application/pdf
- dc.identifier.citation Cozzuto L, Delgado-Tejedor A, Hermoso Pulido T, Novoa EM, Ponomarenko J. Nanopore direct RNA sequencing data processing and analysis using MasterOfPores. Methods Mol Biol. 2023;2624:185-205. DOI: 10.1007/978-1-0716-2962-8_13
- dc.identifier.doi http://dx.doi.org/10.1007/978-1-0716-2962-8_13
- dc.identifier.issn 1064-3745
- dc.identifier.uri http://hdl.handle.net/10230/70086
- dc.language.iso eng
- dc.publisher Springer
- dc.relation.ispartof Methods Mol Biol. 2023;2624:185-205
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-098152-A-100
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PRE2019-088498
- dc.rights This version of the article has been accepted for publication, after peer review (when applicable) and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: http://dx.doi.org/10.1007/978-1-0716-2962-8_13
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.subject.keyword Data analysis
- dc.subject.keyword Direct RNA sequencing
- dc.subject.keyword Nanopore sequencing
- dc.subject.keyword Nextflow
- dc.subject.keyword Open source
- dc.subject.keyword RNA modifications
- dc.subject.keyword Reproducible science
- dc.subject.keyword Workflows
- dc.title Nanopore direct RNA sequencing data processing and analysis using MasterOfPores
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/acceptedVersion