R2Dtool: Positional interpretation of RNA-centric information in the context of transcriptomic and genomic features

Abstract

AbstractLong-read sequencing enables isoform-resolved detection of functionally important RNA elements, such as RNA chemical modifications, RNA secondary structure, or RNA-protein interaction sites. Importantly, the functional impact of these elements can relate to their positions relative to isoform-specific transcript features, such as start and stop codons, open reading frames, exon-exon junctions and transcript termini. Relating transcriptomic and genomic features during sequencing data analysis is challenged by the flexibility of RNA biogenesis and the diversity of alternative mRNA transcripts. To address these challenges and streamline the mapping between transcriptome-mapped data and genome-mapped data, we developed R2Dtool. We illustrate R2Dtool’s capability to process long-read transcriptomic information and potential for interpretation in the context of transcript and genomic annotation features using epitranscriptomics data. R2Dtool embraces and expedites analysis of RNA complexity, and we anticipate it will empower multiple transcriptomic studies for interpretation and discovery. R2Dtool is freely available under the MIT license from https://github.com/comprna/R2Dtool.