Timetable and objectives
In this workshop, we explore RNAseq data preprocessing and analyses for differential expression experiments. Our goal for this workshop is to provide you with foundational knowledge required to understand the basic RNAseq workflow and responsibly apply these methods to your own research.
These sessions will provide you with an opportunity to develop your skills and get exposure to key concepts of RNAseq, practice running nf-core workflows, and performing downstream analyses in RStudio. We have outlined the timetable and learning objectives for each session below:
Lesson plan
| Session | Lesson | Outcomes | Time (min) |
|---|---|---|---|
| 1 | Session 1 kick-off | Discuss session 1 learning objectives, set up CLI environment on Nimbus VMs | 10 mins |
| Introduction to the case study | Explore case study design and objectives | 10 mins | |
| nf-core/rnaseq explained | Discuss RNAseq experimental workflow and nf-core/rnaseq features | 20 mins | |
| Break | ☕ | 10 mins | |
| Raw data QC | Perform raw data quality control and explore outputs | 20 mins | |
| Execute the data preprocessing workflow | Execute full RNAseq data preprocessing workflow and examine nf-core/rnaseq functionality | 30 mins | |
| Read alignment and quantification | Explore outputs of alignment and quantification processes | 10 mins | |
| Break | ☕ | 20 mins | |
| Workflow performance | Evaluate nf-core/rnaseq run technical performance using resource logs and data processing effectiveness using QC metrics | 15 mins | |
| Session 1 wrap-up | Discuss outcomes of data pre-processing and session 2 objectives and activities | 15 mins | |
| 2 | Session 2 kick-off | Discuss session 2 learning objectives, log in to Nimbus VMs | 15 mins |
| Set up Rstudio on Nimbus | Set up Rstudio on Nimbus instances and explore functionality | 15 mins | |
| Break | ☕ | 10 mins | |
| Exploratory analysis | Perform RNAseq count matrix exploratory analysis and evaluate data quality | 40 mins | |
| Break | ☕ | 10 mins | |
| Differential expression analysis | Identify and visualise differentially expressed genes | 20 mins | |
| Functional enrichment analysis | Perform functional enrichment analysis using gene ontologies and pathways | 25 mins | |
| Summarising the experiment | Discuss results of data processing and analysis and experimental outcomes | 15 mins | |
| Session 2 wrap-up | Discuss workshop outcomes, Q&A session | 25 mins |