A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry.

ABSTRACT: Direct RNA sequencing from Oxford Nanopore Technologies (ONT) has become a valuable method for studying RNA modifications such as N6-methyladenosine (m6A), pseudouridine (ψ), and 5-methylcytosine (m5C). Recent advancements in the RNA004 chemistry substantially reduce sequencing errors compared to previous chemistries (e.g., RNA002), thereby promising enhanced accuracy for epitranscriptomic analysis. In this study, we benchmark the performance of two state-of-the-art RNA modification detection models capable of handling RNA004 data - ONT's Dorado and m6Anet - using two wild-type (WT) cell lines, HEK293T and HeLa, with respective ground truths from GLORI and eTAM-seq, and their paired in vitro transcribed (IVT) RNA as negative controls. We found that under default settings and considering si

SUBMITTER: Zou Y 

PROVIDER: S-EPMC11838592 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature