Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line

Genomic DNA used as a template for in vitro transcription of RNA can serve as a true negative control for RNA modification detection in Nanopore direct RNA sequencing (DRS) data. We generated DRS for IVT RNA composed of canonical nucleotides using genomic DNA templates. We applied Dorado modification calling models to these data, which allowed for the calculation of 9-mer specific false positive rates for a set of RNA modifications. These false positive rates capture the complete set of 9-mer sequence contexts and can be applied to a broad range of experimental conditions.