Laura:

SNP identification and analysis is a very complex subject and without knowing 
what you are trying to do it is very difficult to point you to the right 
direction. Perhaps a good place to start would be a supplement for the last 
year's report from 1000 Genomes Consortium (Nature. 467(7319): p. 1061-1073). 
Some of the steps you can perform through Galaxy, yet some are in development. 

Thanks!

anton
galaxy team


On Apr 5, 2011, at 5:19 AM, Laura Iacolina wrote:

> Dear all,
> I’m analysing SNPs data for the first time. I tried with the few software I 
> found in litterature but they can only manage small datasets. I am currently 
> trying with “genetics” package in R but the Geno function takes into account 
> a marker at a time. Considering I have to analyse 200 samples with 50K 
> markers is there any way to tell R to analyse each SNP one after the other?
>  
> Thank you very much for the help.
>  
> Laura
>  
>  
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Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org




___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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  http://lists.bx.psu.edu/

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