Bulk RNASeq: from counts to differential expression
2 days
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.
------------------------------------------------------------------------------------------------------------------------------
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.
- Counting using Galaxy: STAR, htseq-counts, FeatureCounts
- 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
Program
Practical info
29 September 2022 - 04 October 2022
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
29 September 2022 - 04 October 2022
Leuven - Campus Gasthuisberg
29 September 2022 - 04 October 2022
Leuven - Campus Gasthuisberg
Please use Parking West - Follow 'Dagcentrum Onco' to get to the O&N buildings. Take the stairs on you left after exiting Parking West. You are now in front of buidling O&N4 and on the left you find O&N5.
29 September 2022 - 04 October 2022
Leuven - Campus Gasthuisberg
Info for trainer
Elixir code: 7470