Roscoff course 2015 - RAD tags

The practicals are done in two parts:

• A detailed analysis, from raw reads to final results, of a dataset from a paper published in 2013: Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach. The raw dataset is available from the Dryad data archive, doi: 10.5061/dryad.44sf1. We will try to reproduce the results from the paper, criticize the different steps and maybe try different approaches as we go.

  After this part, you should have a general view of a RAD-seq workflow.

• A more specific look at some precise steps of the analysis, using other published datasets. This might entail, for example, genotype calling using a maximum likelihood approach.

During the practicals, we will be using an Etherpad document to share code. You can access the Etherpad document here.

Please follow the links to proceed to the detailed instructions:

• Part one: a complete analysis, from raw reads to results
  • Introduction
  • Raw reads processing
  • De novo assembly
  • Variant calling and genotyping
  • Downstream analysis
    • Phylogeographic tree
    • Mapping back to the threespine genome
    • Prediction of SNP effects in coding regions
    • Genome scan for G_st
    • Gene ontology (GO) enrichment tests
  • Conclusion
• Part two: going further for some analytical steps