Bulk RNASeq: from counts to differential expression
07/06/2024
11/06/2024
General context
The course consists of introductory online material (e-learning) on counting and two face-to-face sessions on differential expression analysis in R and all the questions that arise when trying the analysis on your own data.
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The course will show:
- Tools to generate count files like featureCounts, and htseq count are demonstrated
- Count files from HTSeq-Count, FeatureCounts, Salmon or Kallisto are used to identify differentially expressed genes
On the second day, participants can analyze their own count files. Issues are solved and questions are answered by experts from the VIB Nucleomics Core.
Knowledge of NGS data formats and the first steps in the analysis workflow (fastqc -> bam files). If you are a newbie in the field, you have to follow the NGS introduction training first.
Experience in R programming. If you never worked in R you should attend the R introduction training first. Send a mail to Janick.Mathys@vib.be if you want to attend the R training.
- Counting using Galaxy: STAR, htseq-counts, FeatureCounts, Salmon, Kallisto
- 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: AnnotationDbi
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.
Program
Practical info
07 June 2024 - 11 June 2024
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
07 June 2024 - 11 June 2024
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
07 June 2024 - 11 June 2024
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
07 June 2024 - 11 June 2024
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.
07 June 2024 - 11 June 2024
Ghent - VIB/UGent FSVM II
Room L4 of the FSVM2 building, Technologiepark, Gent