PHINDaccess RNAseq course 2020
Dates, time & location
Dates:
| Day | Date | Time |
|---|---|---|
| 1 | Monday 10th of February 2020 | 9:00-16:30 |
| 2 | Tuesday 11th of February 2020 | 9:00-16:30 |
| 3 | Wednesday 12th of February 2020 | 9:00-16:30 |
| 4 | Thursday 13th of February 2020 | 9:00-16:30 |
Location: Institut Pasteur Tunis
Instructors
| Julia Ponomarenko | Sarah Bonnin |
|---|---|
 |
 |
from the CRG Bioinformatics core facility in Barcelona, Catalonia, Spain.
Material available at https://biocorecrg.github.io/PHINDaccess_RNAseq_2020/
Learning objectives
At the end of the course, the participants will be able to:
- Understand the analysis steps from raw reads to expression counts, differential expression and interpretation of DE genes using the gene set enrichment analysis.
- Find RNA-seq data in public repositories.
- Define a good experimental design, including sequencing parameters and quality control steps.
- Perform quality assessment of RNA-seq data, both raw and computed.
- Understand file formats commonly used in RNA-seq data analysis.
- Gain an overview on common software tools for RNA-seq data analysis and their limitations.
- Perform gene differential expression analysis.
Course Program
- Day 1: Introduction to RNA-seq, experimental design, Start analyzing RNA-seq data: raw data download, quality control, prepare sequencing reads for mapping.
- Day 2: Read mapping to reference genome/transcriptome, UCSC Genome Browser.
- Day 3: Refreshing basics in R. Gene differential expression analysis.
- Day 4: Functional analysis. Independent exercise.
Prerequisites
Familiarity with the Linux command line Familiarity with the R language scripting