Introduction to RAD-seq Data Analysis
Date:
to be determined
Venue:
The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK
Application deadline:
to be determined
Cancellation deadline:
to be determined
Places:
12 (selection of applicants)
Registration fee:
to be determined
Information:
RAD (Restriction site Associated DNA) Sequencing is a method for sampling the genomes of multiple individuals in a population using next generation DNA sequencing. The principal advantage of RAD-seq is the ability to simultaneously examine tens of thousands of genetic loci with vastly reduced sequencing costs versus whole genome approaches. RAD-seq can be used on crosses of any design as well as wild populations and organisms with and without a reference genome. Applications include SNP discovery, linkage mapping and QTL mapping, but also more complex analyses such as population genomic and phylogeographic studies. The aim of this workshop is to familiarise researchers with RAD-seq data and to initiate them in the analysis by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs (e.g. FastQC, BWA, samtools, IGV, Stacks) will be used. In the last section of this workshop we will focus on linkage analysis and population genomics.
"I feel well prepared to begin analysing my RAD-seq data now." (October 2015)
Instructors
Dr. John Davey (Bioinformatician, University of York)
Dr. Judith Risse (Bioinformatician, Wageningen University, The Netherlands)
Workshop format
The workshop consists of presentations and hands-on tutorials.
Who should attend
Graduates, postgraduates, and PIs, who are using or planning to use RAD-seq technology in their research, and want to learn how to process and analyse RAD-seq data.
Requirements
A general understanding of molecular biology and genomics, and elementary skills in computer usage are required.
Covered topics
Introduction to RAD-seq
Introduction to Linux and R
Quality control and demultiplexing of RAD data
Aligning RAD data to a reference
Assembling RAD data de novo
Variant calling
Visualising results
Linkage analysis
Population genomics