A comparative evaluation of computational models for RNA modification detection using nanopore sequencing with RNA004 chemistry.

ABSTRACT: Direct RNA sequencing from Oxford Nanopore Technologies has become a valuable method for studying RNA modifications such as N6-methyladenosine (m6A) and pseudouridine (pseU). Recent advancements in the RNA004 chemistry substantially reduce sequencing errors compared to previous chemistries, promising enhanced accuracy for epitranscriptomic analysis. Here we benchmark the performance of two RNA modification detection models for RNA004 data, Dorado and m6Anet, using two wild-type (WT) cell lines (HEK293T and HeLa), with respective ground truths from GLORI and eTAM-seq, and in vitro transcribed (IVT) RNA as negative controls. We found that for m6A sites with ≥10% modification ratio and ≥ 10X coverage, Dorado has higher recall (~0.92) than m6Anet (~0.51). Among true positive predictions, there

SUBMITTER: Zou Y 

PROVIDER: S-EPMC12346441 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature