There are many interesting patterns that you can extract from genetic variant data. This can include patterns of linkage, balancing selection, or even inbreeding signals. One of the most common approaches is to find sites on the genome that are under selection.
This workshop introduces the basics of genetic selection analysis. It will step you through the process of identifying signals of selection in an example genomic dataset using the outlier analysis method.
Lead Trainer: Dr Katarina Stuart, Research Fellow, University of Auckland.
Date/Time: 27 -28 February 2024, 1pm-6pm NZDT / 11am - 4pm AEDT / 10am - 3pm AEST / 10:30am - 3:30pm ACST / 8am - 1pm AWST (check in your timezone)
Format:
This online workshop will take place over two five-hour sessions. You must attend both sessions as they build on one another. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action.
Learning outcomes:
By the end of the workshop you should be able to:
Download example genomic data
Use the PCAdapt tool to identify outlier loci within a genome.
Use VCFtools to identify outlier SNPs in pairwise population comparisons.
Use Bayescan and Baypass to identify outlier SNPs based on allele frequencies across multiple populations.
Use Baypass to identify SNPs that are related to phenotype (GWAS)
Compare the results of the different methods and discuss the results.
Who the workshop is for:
This workshop is for researchers associated with an Australian organisation and/or members of the Genetics Society of AustralAsia who will use genetic selection analysis as part of their projects.
This workshop requires you to have:
Some familiarity with biological concepts, including the concept of selection.
Basic command line (bash) knowledge. You must know how to navigate the directory structure and copy files between the computers. If you need a refresher on Unix/Linux try this online tutorial.
Basic knowledge of R. You must know how to set up directories, run commands, reading in and outputting files. If you need a refresher on R try the Introduction to R and RStudio section of this online tutorial.
How to apply:
Applications have closed
This workshop is free but participation is subject to application with selection.
Applications close at 11:59pm AEDT, Friday 9 February 2024.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) after the closing date. More information on the selection process is provided in our advice on applying for Australian BioCommons workshops.
This workshop is presented by the Australian BioCommons and the Genetics Society of AustralAsia with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to Australian BioCommons.