Bulk RNA-seq analysis
Bulk RNA-seq analysis
6 October 2026, 09h30-17h00
13 October 2026, 09h00-13h00
General context
Understanding differential gene expression is essential for interpreting RNA sequencing data in modern life sciences. This introductory course is designed for researchers who work with bulk RNASeq data and need to move from raw counts to meaningful biological insights.
Through hands-on sessions, you will learn how to process count files, apply statistical methods in R, and troubleshoot common issues. By the end of the training, you will be equipped to identify differentially expressed genes and confidently analyze your own datasets using widely adopted tools and workflows.
- Explain the principles of bulk RNASeq data processing and differential expression analysis.
- Identify appropriate tools for generating count files, starting from FASTQ files.
- Perform differential expression analysis in R using count data from different quantification tools.
- Interpret output tables and plots to draw biologically meaningful conclusions from differential expression results.
- Troubleshoot common issues encountered during RNASeq data analysis workflows.
The course blends e-learning with hands-on exercises using Galaxy to process raw reads into count files and in-person sessions with hands-on exercises R to identify differentially expressed genes. Both single-end and paired-end example datasets are provided.
Participants complete a homework assignment on either example or personal data, with results and questions reviewed during the final online session.
Experience with R programming. If you have never worked in R, start with our course Basic statistics in R.
- Processing FASTQ files using Galaxy: FASTQC, Trimmomatic, STAR, htseq-counts, FeatureCounts, Salmon, Kallisto, Qualimap, RSEQC
- Identification of DE using Bioconductor: DESeq2 + other packages like tximeta (script for EdgeR is provided but not demonstrated)
- Visualization of results using R: ggplot2, pheatmap
- Mapping of IDs to Gene symbols using Bioconductor: biomaRt
This course is part of the learning paths on Bulk RNAseq data and Single cell data long reads.
Trainers
Janick Mathys
Janick tries to help VIB scientists analyze their data by offering bioinformatics training and support. Next to organizing trainings, creating e-learning courses and teaching statistics, R, Python, Linux, HPC, bulk and single cell RNA-Seq analysis, she consults scientists and develops pipelines for omics analyses. Before joining VIB, she worked as a post-doc at KULeuven, doing research on transcriptomics and transcription regulation. She coordinated the Master of Bioinformatics program of KULeuven and taught the course on Biological Databases.
Practical info
06 October 2026
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
06 October 2026
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
06 October 2026
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
06 October 2026
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.