Bulk RNASeq: from counts to differential expression
This course will show tools to generate count files like featureCounts, and htseq count. 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.
Software demonstrated
- 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
Organised by VIB Technology Training and ELIXIR Belgium