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. |
Thu, 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. |
Fri, 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 Last updated: May 3rd 2019 |