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

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, and 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

SUBMITTER: Bryce-Smith S 

PROVIDER: S-EPMC10327023 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature