The Practice of RADseq: Population Genomics Analysis with Stacks (RDSQ01)
23 September 2019 - 27 September 2019£275.00 - £550.00
This course will focus on population genomics analysis using Stacks version 2 software. The course will include a discussion of RAD sequencing, including the different protocols and the sequencing platforms used. We will focus on the key aspects of the molecular protocol to ensure a successful data analysis. The remainder of the course will include an introduction to UNIX followed by practice with RADseq data analysis. We will focus first on how the major Stacks algorithms work, followed by how to optimize parameters for the software. Next, the course will include two data analyses, a de novo analysis without a reference genome, and an analysis including a reference genome. We assume no bioinformatics experience.
- Acquire the UNIX skills to complete a RADseq analysis
- Learn about RADseq protocols and variations, and sequencing details
- Complete a de novo analysis, including parameter optimization
- Reference genome-based analysis, including a genome scan.
This workshop is aimed at all researchers and technical workers with a background in biology who want to learn RADseq data analysis. The syllabus has been planned with complete beginners in mind.
Venue – PR informatics head office, 53 Morrison Street, Glasgow, G5 8LB – Google map
Availability – 25 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English
We offer COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE ONLY – Includes lunch and refreshments and welcome meal Monday evening.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, refreshments and welcome dinner Monday evening. Self-catering facilities are available in the accommodation. Accommodation is approximately a 6-minute walk from the PR informatics head office. Accommodation is multiple occupancy (max 3-4 people) single sex en-suite rooms. Arrival Sunday 22nd September (between 17:00 – 21:00) and departure Friday 27th September (accommodation must be vacated by 09:15).
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PLEASE READ – CANCELLATION POLICY: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact firstname.lastname@example.org. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees (and accommodation fees if booked through PR informatics) will be credited. However, PR informatics will not be held responsible/liable for any travel fees, accommodation costs or other expenses incurred to you as a result of the cancellation. Because of this PR informatics strongly recommends any travel and accommodation that is booked by you or your institute is refundable, flexible or covered by insurance. It also recommended to delay booking your travel and accommodation as close the course start date as economical viable.
The workshop is delivered over 5 days (see the detailed curriculum listed under course program). Each session consists of a lecture explaining the theory proceeded by a practical based on this lecture. There will also time for students to discuss their own problems and data.
Assumed computer background
We assume no bioinformatics experience.
Equipment and software requirements
A laptop computer with a terminal application. If you own an Apple laptop (or a Linux-based laptop), the Terminal program is already installed. If you own a Windows laptop, please install MobaXterm, or use the Windows Linux Subsytem (if you know how). The computation for the course will take place on the Amazon cloud.
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Meet at 43 Cook Street, Glasgow G5 8JN between 17:00 – 21:00
Monday 23rd – Classes from 09:30 to 17:30
Lecture: Modern sequencing technologies and RAD-seq
Introduction to UNIX
Tuesday 24th – Classes from 09:30 to 17:30
Lecture: Molecular RAD protocols
UNIX, part 2
Cleaning and demultiplexing RAD data
Student Lightning talks
Wednesday 25th – Classes from 09:30 to 17.30
Stacks Parameter optimization
de novo assembly with Stacks for STRUCTURE analysis
Thursday 26th – Classes from 09:30 to 17:30
Referenced-aligned RAD tags for genome scanning and identifying signatures of selection
Friday 27th – Classes from 09:30 to 16:00
de novo assembly of RAD tags with or without a genome for phylogenetic analysis
Lecture: Computer architecture