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ONLINE COURSE – The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) This course will be delivered live
2nd October 2023 - 6th October 2023
£350.00 – £450.00
Event Date
Monday, October 2nd, 2023
COURSE FORMAT
This is a ‘LIVE COURSE’ – the instructor will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link, a good internet connection is essential.
TIME ZONE
TIME ZONE – Central Standard Time – however all sessions will be recorded and made available allowing attendees from different time zones to follow.
About This Course
This course is aimed at introducing researchers to the theory and practice of using reduced representation libraries – such as RAD sequencing – to preform population genomic analysis in non-model organisms. The course will center on running the software pipeline Stacks, focusing on how the characteristics of the underlying molecular libraries result in weak or robust analytical results. Sessions will be live online, consisting of a blend of lectures, interactive demonstrations, and lab practicals, where participants will have the opportunity to ask questions throughout. Computation will be done on the Amazon AWS Cloud.
By the end of the course, participants should be able to:
- Navigate the UNIX file system, execute commands, and interact with bioinformatic data files;
- Understand how to perform a de novo analysis – without a reference genome – including parameter optimization;
- Understand how PCR duplicates and other molecular library characteristics affect analysis;
- Complete a reference genome-based analysis;
- Take the outputs from Stacks to complete a Structure analysis (de novo), a genome scan based on FST(reference-based), and a private allele analysis.
Intended Audiences
Graduate students, post-doctoral researchers, or professionals who wish to learn how to analyze genomic RAD-based data.
Venue
Delivered Remotely
Course Details
Availability – TBC
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English
Teaching Format
Data and analytical approaches will be presented in a lecture format to introduce key concepts. In the beginning, participants will work interactively with the instructor to understand fundamentals. Once completed, the course will shift into a lab practical format, where the instructor introduces the lab, then free time is given for participants to complete the lab with the instructor present to answer questions. At the end of each practical, the instructor will go over the key ideas and results.
Assumed quantitative knowledge
Basic understanding of evolution (mutation, drift, selection, migration, HWE) and population-genomic concepts (e.g., FST, population structure) is assumed.
Assumed computer background
No computational background knowledge is assumed, however, experience in UNIX and/or bioinformatics analysis will enable participants to move at a faster pace.
Equipment and software requirements
Students will need a laptop or desktop with a fast and reliable internet connection. The computer can run any operating system including MacOS, Windows, or Linux, as we will connect, via the terminal, to our AWS instance on the Amazon Cloud.
PLEASE READ – CANCELLATION POLICY
Cancellations/refunds are accepted as long as the course materials have not been accessed,.
There is a 20% cancellation fee to cover administration and possible bank fess.
If you need to discuss cancelling please contact oliverhooker@prstatistics.com.
If you are unsure about course suitability, please get in touch by email to find out more oliverhooker@prstatistics.com
COURSE PROGRAMME
Day 1: 09:00 – 16:00 (Central Standard Time, i.e., Chicago)
- Instructor and participant introductions
- Lecture: Exploring the Genetics of Non-Model Organisms with RAD-seq
- Introduction to the Cloud
- Introduction to UNIX, Part 1
Day 2: 09:00 – 16:00
- Short Lecture: Illumina error model, FastQ files, data quality control, and sample multiplexing
- Cleaning and demultiplexing RAD-seq data
- Introduction to UNIX, Part 2
- Participant two-minute lightning talks
Day 3: 09:00 – 16:00
- Short Lecture: Parameter optimization and de novo assembly of RAD tags
- Understanding the de novo assembly algorithm
- How to optimize assembly parameters in a de novo assembly
- De novo assembly of RAD tags without a genome for a STRUCTURE Analysis
Day 4: 09:00 – 16:00
- Referenced-aligned RAD tags for genome scanning and identifying signatures of selection
- How to perform an integrated analysis – applying de novo data to a related reference genome
Day 5: 09:00 – 16:00
- Short Lecture: Understanding DNA quality, molecular library integrity, and PCR duplicates
- Examining the effects of PCR duplicates in a bird dataset
- Performing a private allele analysis in a hybrid zone
- Open lab, time for questions on participant provided data sets.
Course Instructor
Dr. Julian Catchen is an Associate Professor at the University of Illinois at Urbana-Champaign where he runs a population genomics lab that focuses on how the evolution of the genome affects underlying genomic architecture. He is the primary author of Stacks and has been involved in RADseq analysis since 2009, working on projects in a variety of fishes, birds, and insects while applying a diversity of genomic analyses including defining population structure, conducting genome scans, private allele analysis, and phylogenetics.
Lab Website: https://catchenlab.life.illinois.edu/
Google Scholar: https://scholar.google.com/citations?user=YKnVJaAAAAAJ&hl=en
Research Gate: https://www.researchgate.net/profile/Julian-Catchen
ORCID: https://orcid.org/0000-0002-4798-660X