Whole genome IVT Nanopore DRS
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 data for in vitro transcribed (IVT) RNA composed of canonical nucleotides using genomic DNA from a human cell line. We applied Dorado modification calling models to these data, and calculated 9-mer specific false positive rates for eight RNA modifications. These false positive rates capture all 9-mer sequence contexts and can be applied to a broad range of experimental conditions.