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Citations

18

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Grant support

This work was partly supported by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) (PID2021-128193NB-100 to EMN) and the European Research Council (ERC-StG-2021 No 101042103 to EMN). AD-T is supported by a Severn Ochoa FPI PhD fellowship from the MEIC (PRE2019-088498). We acknowledge the support of the MEIC to the EMBL partnership, Centro de Excelencia Severn Ochoa and CERCA Programme/Generalitat de Catalunya.

Analysis of institutional authors

Cozzuto, LucaCorresponding AuthorDelgado-Tejedor, AnnaAuthorHermoso Pulido, ToniAuthorMaria Novoa, EvaAuthorPonomarenko, JuliaAuthor

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March 20, 2024
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Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores

Publicated to:Crispr Knock-Ins In Organoids To Track Tumor Cell Subpopulations. 2624 185-205 - 2023-01-01 2624(), DOI: 10.1007/978-1-0716-2962-8_13

Authors: Cozzuto, L; Delgado-Tejedor, A; Pulido, TH; Novoa, EM; Ponomarenko, J

Affiliations

Barcelona Inst Sci & Technol, Ctr Genom Regulat CRG, Barcelona, Spain - Author
Univ Pompeu Fabra UPF, Barcelona, Spain - Author

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.

Keywords

Data analysisDirect rna sequencingMessenger-rnaNanopore sequencingNextflowOpen sourceReproducible scienceRna modificationsWorkflows

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Crispr Knock-Ins In Organoids To Track Tumor Cell Subpopulations, Q3 Agency Scopus (SJR), its regional focus and specialization in Genetics, give it significant recognition in a specific niche of scientific knowledge at an international level.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 8.24, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-16, the following number of citations:

  • WoS: 8

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-16:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 10.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 9 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 7.2.
  • The number of mentions on the social network X (formerly Twitter): 12 (Altmetric).

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Cozzuto, LUCA) and Last Author (PONOMARENKO, JULIA).

the author responsible for correspondence tasks has been Cozzuto, LUCA.