Sam's Notebook » Structure http://onsnetwork.org/kubu4 University of Washington - Fishery Sciences - Roberts Lab Thu, 08 Nov 2018 21:47:12 +0000 en-US hourly 1 http://wordpress.org/?v=4.0 Data Analysis – fastStructure Population Analysis of Oly GBS PyRAD Output http://onsnetwork.org/kubu4/2016/08/16/data-analysis-faststructure-population-analysis-of-oly-gbs-pyrad-output/ http://onsnetwork.org/kubu4/2016/08/16/data-analysis-faststructure-population-analysis-of-oly-gbs-pyrad-output/#comments Wed, 17 Aug 2016 02:21:37 +0000 http://onsnetwork.org/kubu4/?p=2251

After some basal readings about what Fst is (see notebook below for a definition and reference), I decided to try to use fastStructure to analyze the PyRAD output from 20160727.

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 program to try to glean some info from these three populations.

 

Jupyter Notebook: 20160816_oly_gbs_fst_calcs.ipynb

 

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