Nanopore-m6A-finder, a novel m6A site caller for Nanopore DRS data

Introduction: A detection methods based on second-generation sequencing, Nanopore direct RNA sequencing (DRS) offers the unique advantage of capturing native modifications. Methods: A prediction computational framework that employs the XGBoost model in the mRNA exonic region and a hard-voting ensemble of XGBoost and random forest models in the poly(A) region. Results and discussion: A site annotation in GLORI v2.0, demonstrating the good performance of our method in the region possessing a stretch of continuous A-sequences. Moreover, our method predicted that m6A might exist in the human HEK293 poly(A) region, suggesting a possibly conserved phenomenon of a modified poly(A) tail beyond the previously reported T. brucei variant surface glycoprotein (VSG) transcripts. Together, these results established NP-mFinder as a robust and versatile tool for transcriptome-wide m6A profiling with DRS data at single-read resolution.