Workshops and courses

ELIXIR node event Scywalker for processing long-read single-cell RNASeq data

View event

Date: 7 October 2026 @ 09:00 - 17:00

Duration: P1DT4H

Language of instruction: English

Loading map...

Understanding transcript diversity at the single-cell level is key when you study gene regulation, cell identity, or disease mechanisms. Traditional short-read sequencing limits your ability to capture isoform variation, which is widespread in complex eukaryotes. You will learn how to interpret the results of Scywalker, a tool designed for processing long-read single-cell RNA-seq data (e.g., ONT or PacBio) to enable full-length transcript analysis. You will follow a step-by-step walkthrough of the Scywalker pipeline to generate gene and transcript count matrices for downstream comparisons of gene and isoform expression across samples and cell types.  The session will include practical instructions on understanding the tool outputs and discussing how to integrate Scywalker results into your single-cell analysis workflows. 

Keywords: Artificial Inteligence, omics

Venue: Antwerp - Campus Drie Eiken UAntwerpen, Universiteitsplein 1

City: Antwerpen

Country: Belgium

Postcode: 2610

Learning objectives:

  • Apply Scywalker to generate gene and transcript count matrices from raw long-read single-cell data
  • Assess the suitability of Scywalker for your own single-cell transcriptomics projects.
  • Explain the content and purpose of each output file generated by Scywalker
  • Interpret Scywalker output to identify gene and isoform expression patterns across samples and cell types
  • Recognize the advantages of long-read sequencing technologies (e.g. ONT PacBio) in capturing isoform diversity
  • “Describe each step of the Scywalker pipeline used for processing long-read single-cell RNASeq data"

Organizer: VIB (https://ror.org/03xrhmk39)

Event types:

  • Workshops and courses

Instructors: Peter De Rijk

Activity log