Roscoff course 2015 - RAD tags

At this point the basic steps which are common to many RAD-seq experiments have been performed:

• raw reads processing (filtering and trimming)
• de novo assembly (or mapping back to a reference if available)
• reads mapping back to the consensus sequences
• variant calling
• genotyping and allele frequency estimates

We are ready to perform the downstream analyses which will answer the biological question(s) that led us to perform the RAD-seq in the first place. Those analyses includes population genomics, phylogeography, phylogenetics, and others.

In this practical the downstream analyses will be:

1. Building a phylogeographic tree of the populations (not demonstrated)
2. Mapping back the consensus sequences to a reference genome
3. Predicting the synonymous or non-synonymous effect of mutations
4. Performing a genome scan using G_st to detect regions of low/high differentiation
5. Test for gene-ontology enrichment in those regions