Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.

ABSTRACT: Polyadenylation is a dynamic process that is important in cellular physiology, which has implications in messenger RNA decay rates, translation efficiency, and isoform-specific regulation. Oxford Nanopore Technologies direct RNA sequencing provides a strategy for sequencing the full-length RNA molecule and analysis of the transcriptome. Several tools are currently available for poly(A) tail length estimation, including well-established methods like tailfindr and nanopolish, as well as more recent deep learning models like Dorado. However, there has been limited benchmarking of the accuracy of these tools against gold-standard datasets. In this article, we present our novel deep learning poly(A) estimation tool-BoostNano-and compare with 3 existing tools-tailfindr, nanopolish, and Dorado. W

SUBMITTER: Chang JJ 

PROVIDER: S-EPMC12406214 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature