In this assignment you will use the skills you learned throughout the subject to analyse and interpret a next generation sequencing dataset. One of the key challenges of this assignment is that you will need to adapt what you have learned in coding exercises and analysis walkthroughs (eg Metagenomics, RNA-seq) to an entirely new dataset. Unlike these earlier assignments no step-by-step instructions are provided so you will need to make many decisions about what analysis to perform and figure out the right commands to make it work. This guide provides information on where to get data and how to structure your assessable work.
Note: Before you proceed. Have you done the metagenomics walkthrough and rnaseq walkthrough? These guides provide a template for you to follow for many (but not all) of the projects listed here.
You should have received an invitation from github to join your personal version of the github repository for this project. You need to accept that invitation and create a new project in RStudio by checking it out from github (like you did for coding assignments).
Choose ONE dataset from the following list.
| Dataset Title | Analysis Type | Complexity | Dataset Link and Instructions |
|---|---|---|---|
| Freshwater turtle microbiome | 16S Metabarcoding | Low | Turtle Data |
| Mouse diets | 16S Metabarcoding | Medium | Mouse Data |
| Oyster microbiome and disease susceptibility | 16S Metabarcoding | High | Oyster Data |
| Coral microbiome and heat stress | 16S Metabarcoding | High | Porites Data |
| Response to sars-cov-2 infection | RNASeq | Medium | COVID Data |
| Heat stress and bleaching in an anemone | RNASeq | High | Anemone Data |
| Genomic signatures associated with Kimberley “super” corals | Variants | Requires genetics knowledge | Coral Variants Data |
| Abalone heat stress | RNASeq (stats only) | Ask before taking this choice | Abalone Data |
Note that each of these datasets is associated with published work. Although you should certainly read the published work to obtain background information on the dataset you are not expected (nor is it always possible) to reproduce the published results. The published results often contain statistical analyses that are beyond the scope of this subject and would take far more time than you have available. Your analysis should focus on a few key techniques that you feel capable of performing and interpreting to a high standard.
You will find that there are many analyses that you could perform with this data. Each dataset comes with a set of suggested analyses specific to that data type. You don’t need to adhere strictly to the suggestions but if you deviate significantly you should discuss this with teaching staff before investing too much time.
For this assignment the assessment for BC5203 differs from BM3331. Please use the links below to find the appropriate assessment guide to your subject: