ADER19F

Analysis of Differential Expression with RNAseq (first course in 2019)

Timetable (provisional)
Mon, June 3rd
Day #1
09:30 - 10:00 Introduction to the course and self presentation of the participants
10:00 - 11:00 The High Throughput Sequencing Workflow. Designing your experiment for Differential Expression using RNA-Seq. Steps in the analysis of RNA-Seq differential expression experiments.
11:00 - 11:30 Coffee Break
11:30 - 12:30 Interpret what are fastq files and what is their content. Use software like FastQC to process fastq files and produce quality reports (QC).
12:30 - 14:00 Lunch Break
14:00 - 16:00 Remove low quality bases, Remove adaptors and other artefactual sequences from your reads.
16:00 - 16:30 Tea Break
16:30 - 18:00 What is a reference genome, versioning and where to obtain genomes. Alignment software: hisat2; bwa; salmon. Run an alignment: the SAM/BAM alignment format.
Tue, June 4th
Day #2
09:30 - 10:00 Morning Wrap-up (what have we done so far?)
10:00 - 11:00 What is a reference gene annotation, versioning and where to obtain. Visualizing alignments in IGV for single genes.
11:00 - 11:30 Coffee Break
11:30 - 12:30 Use Qualimap to assess quality of alignments.
12:30 - 14:00 Lunch Break
14:00 - 16:00 The process of generating gene counts from genome aligments. Use featurecounts to generate tables of gene counts. Use Salmon to generate counts using only the transcriptome.
16:00 - 16:30 Tea Break
16:30 - 18:00 Execute a pairwise differential expression analysis>
Wed, June 5th
Day #3
09:30 - 10:00 Morning Wrap-up (what have we done so far?)
10:00 - 11:00 Interpretation and visualization of results.
11:00 - 11:30 Coffee Break
11:30 - 12:30 Interpretation and visualization of results.
12:30 - 14:00 Lunch Break
14:00 - 16:00 More complex settings: batch effects and paired samples.
16:00 - 16:30 Tea Break
16:30 - 18:00 Gain control over your analysis using R and Rstudio.
Fri, June 6th
Day #4
09:30 - 10:00 Morning Wrap-up (what have we done so far?)
10:00 - 11:00 Specificities of single-cell RNAseq, using the Chromium system as example.
11:00 - 11:30 Coffee Break
11:30 - 12:30 Generate a count matrix for a single-cell RNAseq dataset.
12:30 - 14:00 Lunch Break
14:00 - 16:00 Generate groups of cells by clustering gene expression.
16:00 - 16:30 Tea Break
16:30 - 18:00 Obtain marker genes for the different groups of cells.
Thu, June 7th
Day #5
09:30 - 10:00 Morning Wrap-up (what have we done so far?)
10:00 - 11:00 How to extract meaning from a list of genes.
11:00 - 11:30 Coffee Break
11:30 - 12:30 Understand the concept of functional enrichment analysis, and the statistics involved.
12:30 - 14:00 Lunch Break
14:00 - 16:00 Interpret the results of functional enrichment analysis.
16:00 - 16:30 Tea Break
16:30 - 18:00 Final wrap-up Session
Course Homepage

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated:   May 3rd 2019