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DIY Genetics: Introduction

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Posted 27th December 2011 at 11:11 AM by nathanm

I've been doing my own bio-geographical ancestry (BGA) experiments with the raw data from my mother's and my Family Finder (FF) tests and my father's from 23andMe. What got me started was reading the various genome bloggers who have BGA projects. I don't meet the criteria for inclusion in any of them, but did get my dad into the Eurogenes Genetic Ancestry Project, the newer Artemis Project, and later the Dodecad Ancestry Project. This was well before Dienekes first released the DIYDodecad program, so it was about the only option for further analyzing my autosomal DNA. I'd already had Dr McDonald run his analysis, but it didn't add much detail.

Fortunately, one of the genome bloggers, Razib Khan, posted a step-by-step tutorial for running Admixture, complete with links to a reference dataset. It assumes a fairly technical background and comfort with the command line. I first read through Razib's tutorial, downloaded the software and data, and went through his exact steps in April. It didn't work at first, but through much trial and error, I was able to get it to run properly. Then in May, I did some initial experiments of my own, adding my own data to the analysis and mixing and matching various populations from the reference dataset. Since then, I've fiddled with it off and on every few weeks, but I wasn't satisfied with either the results, or my understanding of them, until recently. Before I explain how to do it, I'll write a post with the results of one of my first successful experiments.
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  1. Old Comment

    Hardware, Operative System, Software

    Could you describe what hardware(s) and operative system(s) and perhaps software(s) that you are using in order to create an environment suitable for ADMIXTURE-associated work (raw data, input files, analyses, result files, interpretations etc.)?
    Posted 30th December 2011 at 06:06 AM by Marbom Marbom is offline
  2. Old Comment

    Hardware, Operative System, Software

    Quote:
    Originally Posted by Marbom View Comment
    Could you describe what hardware(s) and operative system(s) and perhaps software(s) that you are using in order to create an environment suitable for ADMIXTURE-associated work (raw data, input files, analyses, result files, interpretations etc.)?
    Yes, that'll be my next post. Stay tuned...
    Posted 30th December 2011 at 09:40 PM by nathanm nathanm is offline
 

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