DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using Nanopore direct RNA sequencing

Single-molecule detection and phasing of A-to-I RNA editing events remains an unresolved problem. Long-read and PCR-free Nanopore native RNA sequencing offers a great opportunity for direct RNA editing detection. Here, we develop a neural network model, DeepEdit, that not only recognizes A-to-I editing events in single reads of Oxford Nanopore direct RNA sequencing, but also resolves the phasing of RNA editing events on transcripts. We illustrate the robustness of DeepEdit by applying it to Schizosaccharomyces pombe and Homo sapiens transcriptome data. We anticipate DeepEdit to be a powerful tool for the study of RNA editing from a new perspective.