Structure vs. Faststructure for large SNP GBS data

[Swati Puranik]

Hello,

From the perspective of a biologist (and not a bioinformatician) with no computational background and limited support staff for training and collaborating, could I please request an opinion from the group members? For a SNP data that I have of 157000 SNPs from 200 individuals, could I use Structure which has a Windows based GUI? Doesn't matter the time it takes as long as it gets the job done!

Thank you.
Regards
Swati

[Vinod Kumar]

But why you want to include all these SNPs, your final information may be misleading due to LD, and window version won't work with such a huge dataset unless you have a supercomputer. I think, it's a wastage of time.

Thanks,

Swati

--
You received this message because you are subscribed to the Google Groups "structure-software" group.
To unsubscribe from this group and stop receiving emails from it, send an email to structure-softw...@googlegroups.com.
To post to this group, send email to structure...@googlegroups.com.
Visit this group at https://groups.google.com/group/structure-software.
For more options, visit https://groups.google.com/d/optout.

--

Vinod Kumar, Post Doctoral Fellow, UMR INRA – Agrocampus Ouest – Université Rennes 1 Institut de Génétique, Environnement et Protection des Plantes Tel : 07-68-32-37-38, Email: Vinod...@rennes.inra.fr INRA,UMR 1349, IGEPP, BP35327, F-35653 Le Rheu, France

Centre de Rennes Domaine de la Motte - BP 35327 35653 Le Rheu cedex - France www.rennes.inra.fr/igepp

[zeamne T]

Have to agree with Vinod on this. Better if you subsample the data set.