Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models.

ABSTRACT: In recent years, nanopore direct RNA sequencing (DRS) became a valuable tool for studying the epitranscriptome, owing to its ability to detect multiple modifications within the same full-length native RNA molecules. Although RNA modifications can be identified in the form of systematic basecalling "errors" in DRS data sets, N6-methyladenosine (m⁶A) modifications produce relatively low "errors" compared with other RNA modifications, limiting the applicability of this approach to m⁶A sites that are modified at high stoichiometries. Here, we demonstrate that the use of alternative RNA basecalling models, trained with fully unmodified sequences, increases the "error" signal of m⁶A, leading to enhanced detection and improved sensitivity even at low stoich

SUBMITTER: Diensthuber G 

PROVIDER: S-EPMC11610583 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature