Mapping of RNA Modifications by Direct Nanopore Sequencing and JACUSA2

RNA modifications exist in all kingdom of life. Several different types of base or ribose modifications are now summarized under the term "epitranscriptome." With the advent of high-throughput sequencing technologies, much progress has been made in understanding RNA modification biology and how these modifications can influence many aspects of RNA life. The most widespread internal modification on mRNA is m6A, which has been implicated in physiological processes as well as disease pathogenesis. Here, we provide a workflow for the mapping of m6A sites using Nanopore direct RNA sequencing data. Our strategy employs pairwise comparison of basecalling error profiles with JACUSA2. We outline a general strategy for RNA modification detection on mRNA and describe two specific use cases on m6A detection in detail. Use case 1: a sample of interest with modifications (e.g., "wild-type" sample) is compared to a sample lacking a specific modification type (e.g., "knockout" sample, here METTL3-KO) or Use case 2: a sample of interest with modifications is compared to a sample lacking all modifications (e.g., in vitro transcribed cDNA). We provide a detailed protocol on experimental and computational aspects. Extensive online material provides a snakemake pipeline to identify m6A positions in mRNA and to validate the results against a miCLIP-derived m6A reference set. The general strategy is flexible and can be easily adapted by users in different application scenarios.