Outlier Analysis Workshop in-person
Identify regions of the genome that are under forms of selection using outlier analysis in this two-day, in-person workshop.
Date and time
Location
About this event
This in-person workshop is delivered by Genomics Aotearoa and NeSI, and will be taught over two consecutive days from 10:00am-4:00pm NZT on the 9th and 10th of August 2023 and is for New Zealand researchers interested in signals of selection in genomes. The workshop will be held in Auckland.
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 outliers 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.
We encourage you to bring your own data! For participants who do not have their own data, a group dataset is available and will be used by the instructors during the examples.
During this workshop you will:
- Download example genomic data (or prepare your own).
- 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 an in-person, hands-on workshop. This 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 laptops and plan to participate actively. You will require a working web browser.
If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.