Exploring GBS data and some file conversions

I’ve been working on organizing my scripts to analyze GBS data for my dissertation chapter¬†on the phylogeography of the Olympia oyster. Still a lot of work to do, but here’s a couple of notebooks. All notebooks can be found at my Github under 2016_Notebooks and the scripts referenced in them can be found in my Github’s Scripts repository.

GBS_File_Conversions.ipynb: I’m planning on using this notebook¬†to describe various file conversion scripts and code snippets I’ve written to work with. May end up splitting them into separate notebooks, but we’ll see. Currently, it describes how to add population information to the Structure (.str) output from ipyrad/pyrad, whether that be integers (required by the actual Structure program), or strings (useful for programs like Adegenet in R). It also describes how to take a .geno or .str file and split it up into many .geno files for looking at pairwise Fst and nucleotide diversity in R.

Exploring_GBS_Data_With_R.ipynb: This notebook has snippets of code used to explore pairwise Fst and nucleotide diversity (pi). Will eventually expand to include other R-based analysis methods.


FST and Admixture Ananlysis of 2bRAD Subset

I did a quick FST and Admixture analysis of the subset of 20 individuals from each population (19 from SS as one of them had inconsistent genotyping across replicates). You can view the results at this Jupyter Notebook on my github. These are very preliminary and will likely benefit from more individuals and by playing around more with the parameters in the mapping/genotyping. I plan to also look at nucleotide diversity.