Workshop: Outlier Analysis
On 09-10 August 2023, from 10:00am to 4:00pm, NeSI and Genomics Aotearoa will be co-hosting a workshop on Outlier Analysis. This workshop is for New Zealand based researchers interested in signals of selection in genomes.
The focus of this workshop is on identifying signals of selection in an example genome using the outlier analysis method. Outlier analysis assumes that the majority of the genome is under neutral selection and some loci will appear as outlier relative to this background.
This lesson assumes learner has no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of selection. You are expected to have some familiarity with both the R programming language and with basic command line (bash). If you need to refresh, please revise the material in our previous workshops on R and bash.
During this workshop you will:
- Download example genomic data.
- Use the PCAdapt tool to identify outlier loci within a genome.
- Use VCFtools to identify outlier SNPS in population comparisons.
- Use Bayescan to identify outlier SNPS based on allele frequencies.
- Relate identified SNPS to phenotypic variation.
- Compare the results of the different methods and discuss the results.
Setup
This is a fully online, hands-on workshop. The workshop material will be run on the NeSI High Performance Computing (HPC) platforms - there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.
Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.
If you have any questions about this workshop, including whether it is suitable for you, please contact training@nesi.org.nz OR tyler.mcinnes@otago.ac.nz
