This three-day course will provide an overview of the RNA-seq analysis pipeline, as well as the downstream analysis of the resulting data using bioconductor packages in R. The course will cover the following topics:

  • The structure of an RNAseq analysis pipeline:
    • Raw data quality check;
    • RNAseq reads alignment;
    • Gene Expression level quantification and normalization by reads counting;
    • De novo Transcripts reconstruction and differential splicing.
  • Overview of downstream analysis
    • Differential Expression analysis with R/Bioconductor packages;
    • Class discovery: usage of Principal Component Analysis, Clustering, Heatmaps, Gene Set Enrichment Analysis in RNA-seq analysis.

Next Generation Sequencing (NGS) techniques will not be covered in this course; experimental design as well as the statistical methods will not be detailed in this course.