On Mon, Dec 31, 2012 at 2:03 PM, Goldberg, Arthur P <arthur.p.goldberg@mssm.edu> wrote:

We have SNP microarrays about hundreds of subjects. In particular, samples were processed on the Illumina Infinium HumanExome BeadChip, with 951,117 markers.. Our project is collaborative, so we've a couple of dozen users in multiple countries. I'm happy to run my own Galaxy instance and create user accounts.

But I need to be able to upload tables (in tsv files) describing the subjects, with attributes such as IDs, phenotype, gender, age, etc. And then I want to associate data files (idat, GenomeStudio genotype, etc.) with the subjects. Does Galaxy support this functionality, or can I add it easily?

A default installation can do a lot with TSV files, so I think that part is easy.

Can you provide more information on how you want to associate the files? What will that association look like? If you just want file names in additional columns, then I think that should be workable too.

If you are looking for more sophisticated bundling, Galaxy does have support for complex data types where you can bundle together multiple files, but I haven't worked with it yet, and I suspect it is non-trivial. (Can someone on the list comment on that?)

Feel free to forward this email if you're not the right person to answer it.

I did! I have forwarded this to the Galaxy development list.

Thanks,

Dave C.

BR
A

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Arthur Goldberg
Associate Professor of Psychiatry
Seaver Autism Center - Mount Sinai School of Medicine
Seaver Center, Room ABE-33
212-241-4229
Arthur.Goldberg@mssm.edu