Schedule

Schedule

Day1:
9:15 - 10:30:  - Introduction to RNA-sequencing
                       - Experimental design: challenges, considerations, strategies
                       - Examples
10:30 - 11:00: Coffee Break
11:00 - 12:30: - Sequencing archives, SRA, ENA and DDBJ
                        - Practicals using SRA-tools
                        - File format - Quality Control - subsetting
12:30 - 13:30: Lunch break
13:30 - 15:00: - Interpretation of a Fastqc report and acting upon for cutting/trimming reads
                        - Trimming/filtering quality control - Practicals
15:00 - 15:30: Coffee break
16:00 - 17:00: - Alignment to a reference genome/transcriptome
                        - TopHat
                        - STAR

Day2:
9:00 - 10:30: Expression quantification:
                       - FPKM (Fragments Per Kilobase Of Exon Per Million fragments mapped) vs. Counting mapped fragments
                       - Practicals using htseq-count
10:30 - 11:00: Coffee Break
11:00: 12:30: Differential expression
                      -Practicals using DESeq2 (R-statistics)
12:30 - 13:30: Lunch Break
13:30 - 15:00: Gene Ontology and GO enrichment analysis
                          - practicals using Goseq (R-statistics)
15:00 - 15:30: Coffee break
15:30 - 17:00: Differentially enriched Pathways finding
                           - practicals using Pathview (R-statistics)

17:00- 17:30: Optional exam