Understanding transcript diversity at the single-cell level is increasingly important for researchers studying gene regulation, cell identity, and disease mechanisms. Traditional short-read sequencing methods limit insights into isoform variation, which is widespread in complex eukaryotes. 

This training introduces Scywalker, a tool for processing long-read single-cell RNA-Seq data (e.g., ONT or PacBio) to enable full-length transcript analysis. Aimed at researchers, postdocs, and bioinformatics support staff working with single-cell data, the course provides a step-by-step walkthrough of the Scywalker pipeline and its outputs. The tool was designed to generate gene and transcript count matrices that can be used for downstream comparisons of gene and isoform expression across samples and cell types. By the end of the course, attendees will be equipped to use and interpret the Scywalker output and assess the benefits of long-read sequencing in single-cell transcriptomics.