Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.

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Bryce-Smith, Sam, Burri, Dominik ORCID: 0000-0002-8131-9309, Gazzara, Matthew R, Herrmann, Christina J ORCID: 0000-0003-1649-3463, Danecka, Weronika, Fitzsimmons, Christina M, Wan, Yuk Kei, Zhuang, Farica, Fansler, Mervin M, Fernández, José M et al (show 16 more authors) , Ferret, Meritxell, Gonzalez-Uriarte, Asier, Haynes, Samuel, Herdman, Chelsea, Kanitz, Alexander, Katsantoni, Maria, Marini, Federico, McDonnel, Euan, Nicolet, Ben ORCID: 0000-0002-0065-7729, Poon, Chi-Lam, Rot, Gregor, Schärfen, Leonard ORCID: 0000-0003-0234-7609, Wu, Pin-Jou, Yoon, Yoseop ORCID: 0000-0002-6062-0979, Barash, Yoseph ORCID: 0000-0003-3005-5048 and Zavolan, Mihaela ORCID: 0000-0002-8832-2041 (2023) Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data. RNA (New York, N.Y.), 29 (12). pp. 1839-1855.

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Abstract

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3'-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for continuous extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies, while the containers and reproducible workflows could easily be deployed and extended to evaluate new methods or data sets.

Item Type:	Article
Uncontrolled Keywords:	RNA, Sequence Analysis, RNA, Polyadenylation, Benchmarking, RNA-Seq
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Tech, Infrastructure and Environmental Directorate
Depositing User:	Symplectic Admin
Date Deposited:	09 Apr 2024 08:59
Last Modified:	09 Apr 2024 13:28
DOI:	10.1261/rna.079849.123
Open Access URL:	http://10.0.4.237/rna.079849.123
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3180170