Arun, if you have a plink format genotype file (pbed is best -
compressed) in your history, it should appear among the input files
for the eigenstrat tool - it seems to be ok on Main right now.
They can be uploaded using the get data upload tool - you have to
manually set the datatype to pbed so the three file parts can be
The eigensoft tool uses a subset since WGA SNPs contain a lot of
redundant information - an LD independent set is more efficient and
loses little information.
If you select a pbed it should be automatically converted - and run
more quickly the second time
On Tue, Jul 13, 2010 at 12:03 AM, <galaxy-user-request(a)lists.bx.psu.edu> wrote:
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Date: Fri, 9 Jul 2010 13:37:16 -0400
From: "Arun Tiwari" <Arun_Tiwari(a)camh.net>
Subject: [galaxy-user] Rgenetics tool
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I was wondering in what format should I upload my genotype data file obtained from PLINK.
I tried uploading the binary file (bed, bim, fam) as wellas the ped/map file but I am
unable to run any analysis as they never appear in the input file section. I wanted to run
eigenstrat using the rgenetics tools for my data.
Thanks a lot for your help,
Centre for Addiction and Mental Health,