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 uploaded together. 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@lists.bx.psu.edu wrote:
Send galaxy-user mailing list submissions to galaxy-user@lists.bx.psu.edu Message: 7 Date: Fri, 9 Jul 2010 13:37:16 -0400 From: "Arun Tiwari" Arun_Tiwari@camh.net To: galaxy-user@bx.psu.edu Subject: [galaxy-user] Rgenetics tool Message-ID: ACF8150B8AE2E042834D0198F418098040AB99@camhems-4.camh.ca Content-Type: text/plain; charset="iso-8859-1"
Hello,
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