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.