The recent advent of Nanopore sequencing allows for the sequencing of full-length RNA or cDNA molecules. This new type of data introduces new challenges from the computational point of view, and requires new software as well as dedicated analysis pipelines. In this chapter, we guide the reader through the typical analysis steps required to process the raw data produced by the instrument into a table of counts suitable for downstream analyses. We first describe the procedure to convert raw direct RNA-Seq and cDNA-Seq data into sequences in fastq format. We then outline how to perform quality control and filtering steps and how to map the filtered long reads to a reference transcriptome or genome.
Keywords: Bioinformatics; Direct RNA sequencing; Nanopore; Transcriptomics; cDNA sequencing.