---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2016-08-17 02:21:37+00:00
layout: post
slug: data-analysis-faststructure-population-analysis-of-oly-gbs-pyrad-output
title: Data Analysis - fastStructure Population Analysis of Oly GBS PyRAD Output
categories:
  - 2016
  - Genotype-by-sequencing at BGI
tags:
  - fastStructure
  - jupyter notebook
  - olympia oyster
  - Ostrea lurida
  - Structure
---

After some basal readings about what Fst is (see notebook below for a definition and reference), I decided to try to use [fastStructure](https://rajanil.github.io/fastStructure/) to analyze the PyRAD output from [20160727](https://robertslab.github.io/sams-notebook/posts/2016/2016-07-27-data-analysis-pyrad-analysis-of-olympia-oyster-gbs-data/).

The quick, TL;DR: after spending a bunch of time installing the program, it doesn't handle the default Structure file (.str); requires some companion file types that PyRAD doesn't output.

I've put this here for posterity and background reference on Fst...

Will proceed with using the full blown [Structure](https://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/html/install.html) program to try to glean some info from these three populations.



Jupyter Notebook: [20160816_oly_gbs_fst_calcs.ipynb](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20160816_oly_gbs_fst_calcs.ipynb)
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