Prerequisites
All pre-requisites are taken care of if you are using this lesson at the Otago Bioinformatics Spring School 2021.
This RNA-seq workshop aims to get you started with your own RNA-seq analysis and assumes you are already familiar with the basics of bash and R.
This workshop is sponsored by Genomics Aotearoa and the New Zealand eScience Infrastructure (NeSI).
| Setup | Download files required for the lesson | |
| 00:00 | 1. Workshop Overview |
What is RNA-seq?
What data will we be using in this workshop? |
| 00:40 | 2. Quality control of the sequencing data. | What tools do we use to assess the data quality data in RNA-seq experiments? |
| 01:10 | 3. Trimming and Filtering reads | What steps are required for basic data cleaning in RNA-seq studies? |
| 01:40 | 4. Map and count reads | How do we turn fastq data into read counts? |
| 02:25 | 5. Differential Expression | How can we identify genes which exhibit changes in expresion between experimental conditions? |
| 03:40 | 6. Overrepresentation analysis (Gene Ontology) | How can we identify changes in biological mechanisms (e.g., pathways) in gene expression studies? |
| 04:40 | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.