Scywalker for processing long-read single-cell RNASeq data
Scywalker for processing long-read single-cell RNASeq data
7 October 2026, 13h00-17h00
General context
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.
- Describe each step of the Scywalker pipeline used for processing long-read single-cell RNASeq data.
- Explain the content and purpose of each output file generated by Scywalker.
- Recognize the advantages of long-read sequencing technologies (e.g., ONT, PacBio) in capturing isoform diversity.
- Interpret Scywalker output to identify gene and isoform expression patterns across samples and cell types.
- Assess the suitability of Scywalker for your own single-cell transcriptomics projects.
The session will include practical instructions on understanding the tool outputs and discussing how to integrate Scywalker results into your single-cell analysis workflows.
This course is part of the learning path Single cell data long reads.
AI methods used
The course covers machine learning methods for high-dimensional transcriptomics data analysis, including dimensionality reduction and clustering techniques for identifying patterns and structure in complex datasets. These methods are demonstrated in the context of long-read single-cell RNA sequencing data.
Trainers
Peter De Rijk
Dr. Peter De Rijk is responsible for the analysis of the data generated by Nanopore sequencing. To this end he develops and upkeeps the analysis pipelines and he is involved in analysis consulting, implementation, benchmarking and troubleshooting.
Practical info
07 October 2026
Antwerp - Campus Drie Eiken UAntwerpen
Universiteitsplein 1
2610 Antwerpen
Belgium
07 October 2026
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp has a dense public transportation network. Buses and trams are available to take you to many different parts of the city. There are direct bus links to various other towns and cities as well. Plan your route using the De Lijn timetables.
- Campus Middelheim - Campus Groenenborger: around 7 min. on foot
- Campus Middelheim - Campus Drie Eiken: around 35 min.
- Campus Groenenborger - Campus Drie Eiken: around 45 min.
- Stadscampus - Campus Middelheim: around 45 min.
- Stadscampus - Campus Groenenborger: around 55 min.
- Stadscampus - Campus Drie Eiken: around 60 min.
Did you know Antwerp also has a water bus? You can use it to travel between the Antwerp city centre and nearby towns.
07 October 2026
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp is a bike-friendly city. Get to know the smart and cheap way to travel around in Antwerp fot students.
For short trips in and around the city, a rental bike is ideal. Apart from the student bicycle and the Velo city bikes, there are several other bike rental options.
Do you need to cross the Scheldt? Check the availability of the bike lifts and escalators of the tunnels, or take Antwerp’s ferry service with your bike.
Cycling between campuses:
- Stadscampus - Campus Middelheim: 20 min.
- Stadscampus - Campus Groenenborger: 25 min.
- Stadscampus - Campus Drie Eiken: 30 min.
- Campus Middelheim - Campus Groenenborger: 4 min.
- Campus Middelheim - Campus Drie Eiken: 10 min.
- Campus Groenenborger - Campus Drie Eiken: 8 min.
The newest way to travel around Antwerp is by shared electric scooter.
07 October 2026
Antwerp - Campus Drie Eiken UAntwerpen
It’s recommended to travel to and in Antwerp by public transport. If you are travelling by car, take the following into account:
- There are P+R zones where you can park on various main roads into Antwerp. They are ideal places to switch to bus, tram or bike a few kilometres from the campus.
- The Antwerp city centre and part of Linkeroever (Antwerp’s left bank) are a low-emission zone: highly polluting vehicles are not allowed into the city.
- Keep in mind that the zone around the Stadscampus is a residential area with a speed limit of 20 km/h. Pedestrians freely make use of the entire road.
- Take possible road works and events into account.
- Within Antwerp, you can make use of the taxi service.
Campus Drie Eiken en Campus Groenenborger have free university parking spots.
Carpooling is not only fun and ecological, but also good for your wallet and you get to meet new people. Are you looking for a car ride or a fellow passenger, occasionally or daily? Take a look at our carpool platform.