e-learning
RAD-Seq Reference-based data analysis
Abstract
In the study of Hohenlohe et al. 2010, a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback Gasterosteus aculeatus was conducted. Authors used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How to analyze RAD sequencing data using a reference genome for a population genomics study?
Learning Objectives
- Analysis of RAD sequencing data using a reference genome
- SNP calling from RAD sequencing data
- Calculate population genomics statistics from RAD sequencing data
Licence: Creative Commons Attribution 4.0 International
Keywords: EBV dataset, EBV workflow, Ecology, Genetic composition EBV class, RAD-seq, Species population EBV class
Target audience: Students
Resource type: e-learning
Version: 11
Status: Active
Prerequisites:
Introduction to Galaxy Analyses
Learning objectives:
- Analysis of RAD sequencing data using a reference genome
- SNP calling from RAD sequencing data
- Calculate population genomics statistics from RAD sequencing data
Date modified: 2024-06-27
Date published: 2017-02-14
Contributors: Yvan Le Bras
Scientific topics: Ecology
Activity log
