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:
> Send galaxy-user mailing list submissions to
> Message: 7
> Date: Fri, 9 Jul 2010 13:37:16 -0400
> From: "Arun Tiwari" <Arun_Tiwari(a)camh.net>
> To: <galaxy-user(a)bx.psu.edu>
> Subject: [galaxy-user] Rgenetics tool
> Message-ID: <ACF8150B8AE2E042834D0198F418098040AB99(a)camhems-4.camh.ca>
> Content-Type: text/plain; charset="iso-8859-1"
> 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,
> Arun Tiwari
> Centre for Addiction and Mental Health,
> Toronto, Canada