Otago Bioinformatics Spring School 2026
RNA-seq Data Analysis
Workshop schedule
Thursday 19th November, 2026
| Approx time | Item |
|---|---|
| 09:30 - 09:45 | An overview of RNA-seq data analysis workflows |
| 09:45 - 10:30 | Sequence Quality |
| 10:30 - 10:50 | BREAK |
| 10:50 - 12:15 | Index, align and quantifying gene expression |
| 12:15 - 13:00 | LUNCH |
| 13:00 - 13:30 | RNA-seq presentation by Dr Stephanie Waller |
| 13:30 - 14:30 | Identifying differentially expressed genes |
| 14:30 - 14:50 | BREAK |
| 14:50 - 16:00 | Functional analysis |
| 16:30 | END OF DAY |
What’s covered in this workshop
- Full RNAseq workflow of a New Zealand endemic species using both bash and R tools.
- Illumina short-read quality assessment and pre-processing.
- Aligning paired-end reads to a publically available genome.
- Identifying differentially expressed genes with DEseq2.
- Functional annotation using GOseq to investigate trends in expression.
What’s not covered in this workshop
- Submitting and optimising HPC scheduled jobs (see Bash scripting and HPC Job Scheduler workshop)
- Extensive data manipulation and plotting in R, beyond the basics.
Setup
During the workshop, code will be run in real-time to demonstrate the analysis. This will be run on the REANNZ OpenOnDemand HPC platform which already has all the required software and R packages installed.
Attribution notice
This workshop is based on an existing Genomics Aotearoa RNAseq workshop, shortened to fit in one day. Further attribution context is described in that workshop.
