• Event
  • Scientific training

Population Variation Genetics

This course will discuss the RAD molecular protocol and the computational analysis of RAD data using Stacks.

Start date:

22 May 2017

End date:

26 May 2017

Time:

12h00 - 15h30

Venue:

Earlham Institute

Registration deadline:

16 April 2017

Cost:

£600.00

About the event.

To familiarise students with the molecular and analytical aspects of the genetic screening method Genotype-By-Sequencing (GBS).  

GBS involves the use of short-read sequence data produced from Reduced Representation Libraries (RRL), such as Restricted Site Associated DNA (RAD-tags). GBS libraries can provide a dense set of single nucleotide polymorphisms.

SNP markers are spread evenly across a genome. These markers are useful for a variety of genetic and genomic analyses in both model and non-model organisms. Students will gain experience with the computational pipeline 'Stacks' which was designed for the analysis of such data.

The course will focus on the necessary UNIX skills to handle GBS data, as well as how to clean and demultiplex Illumina sequences. Students will then analyse RAD-seq data de novo to perform a population analysis without the aid of a reference genome using Stacks and structure, and from an organism with a reference genome to generate Fst measures and identify signatures of selection.

Course Prerequisites

Those accepted will be in the planning stages, or producing a Genotype-By-Sequencing project.

Target audience

Graduate students, post-docs and PI's.

Programme.

Day 1 - 22 May 2017

Time

Topic

12:00 - 12:45

Registration and lunch

12:45 - 13:15

Welcome, introduction and EI

13:15 - 14:30

Getting to know each other – trainee presentations

14:30 - 15:00

Coffee break

15:00 - 16:00

Introduction to Modern Sequencing Technologies

16:00 - 17:30

Part 1: Introduction to UNIX

17:30 - 18:30

Poster session with pizza and beer

18:30 - 19:30

Part 2: Introduction to UNIX

Day 2 - 23 May 2017

Time

Topic

09:00 - 10:30

Part 3: Introduction to UNIX

10:30 - 11:00

Coffee break

11:00 - 13:00

Part 4: Introduction to UNIX

13:00 - 14:00

Lunch

14:00 - 14:30

Introduction to RAD-seq

14:30 - 15:00

Mini-lecture: quality control, cleaning and demultiplexing RAD-seq data

15:00 - 16:00

Part 1: RAD-seq lab – cleaning and demultiplexing RAD-seq data

16:00 - 16:30

Coffee break

16:30 - 17:30

Part 2: RAD-seq lab – cleaning and demultiplexing RAD-seq data

17:30 - 19:00

Dinner

19:00 - 20:30

RAD-seq case studies and experimental considerations

Day 3 - 24 May 2017

Time

Topic

09:00 - 10:30

RAD-seq lab: double digest and paired end RAD-seq data

10:30 - 11:00

Coffee

11:00 - 13:00

Part 1: RAD-seq lab: working without a reference genome: understanding parameters and methods

13:00 - 14:00

Part 1: RAD-seq lab: working without a reference genome: understanding parameters and methods

14:00 - 15:00

Guest lecture

15:00 - 16:00

Mini-lecture: de novo map and stacks parameters

16:00 - 16:30

Coffee break

16:30 - 18:00

Part 2: RAD-seq lab: working without a reference genome: understanding parameters and methods

19:30 - 21:30

Course dinner

Day 4 - 25 May 2017

Time

Topic

09:00 - 09:15

Mini-lecture: Genome alignment and SNP calling

09:15 - 11:00

Part 1: RAD-seq lab: working with a reference genome

11:00 - 11:30

Coffee break

11:30 - 12:45

Part 2: RAD-seq lab: working with a reference genome: FST genome scans

12:45 - 13:45

Lunch

14:00 - 15:00

Guest Lecture

15:00 - 15:30

Mini-lecture: phylogenetic analysis with RAD-seq

15:30 - 16:00

Coffee break

16:00 - 18:30

Part 1: RAD-seq lab - Phylogenetic analysis

Day 5 - 26 May 2017

Time

Topic

09:00 - 10:30

Part 2: RAD-seq lab - Phylogenetic analysis

10:30 - 11:00

Coffee break

11:00 - 12:00

Part 3: RAD-seq lab - Phylogenetic analysis

12:00 - 13:00

Lunch

13:00 - 14:45

Sequencing Technologies and tour of EI facilities

14:45 - 15:00

Feedback and Wrap up

15:00 - 15:30

Coffee and departure

Fees and accommodation.

Registration costs are inclusive of lunch and refreshments, course dinner and course materials. Accommodation and transport from/to hotel to EI will be an optional extra during registration to book if you are selected for the course.

Related reading.