Question: Sample Cel File Dataset For Affymetrix Axiom Genotyping Platform
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gravatar for pufferfish
6.7 years ago by
pufferfish260
South Africa
pufferfish260 wrote:

I'm looking for a dataset that can be used to test students' ability to do genotype calling using the Affymetrix Power Tools pipeline.

As such, it should ideally:

  • come with known genotypes
  • contain more than one ancestral group (for testing ability to find structure etc)
  • not be too well known,

..although none of theses are dealbreakers

I've tried:

  • the Affy website: only seems to have called genotypes
  • The Broad Institute website
  • 1000 genomes data server

None of these resources seem to make this sort of dataset available, although they must have them internally. Any advice?

EDIT: To be clear, I'm looking for Axiom data, not SNP6

affymetrix • 4.3k views
ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by pufferfish260
1
gravatar for Matt Shirley
6.7 years ago by
Matt Shirley9.3k
Cambridge, MA
Matt Shirley9.3k wrote:

You'll find plenty of Affy 6.0 CEL files on the HapMap FTP site. You'll also find genotypes on the same site as well. This file maps the naming scheme to HapMap NA accessions. You'll also be able to determine the ancestral groups from this file.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Matt Shirley9.3k

Thanks, but I'm looking for Axiom data. Mentioned in the title and have now added to the question text

ADD REPLYlink written 6.7 years ago by pufferfish260

Sorry, I didn't catch that. It seems that Affymetrix does supply 90 Axiom Exome319 CEL files for the HapMap YRI population.

ADD REPLYlink written 6.7 years ago by Matt Shirley9.3k
1
gravatar for Peixe
6.7 years ago by
Peixe600
Spain
Peixe600 wrote:

Have you tried the GEO Datasets? Don't know much about it, but i remember once I did a similar exercise with it...

ADD COMMENTlink written 6.7 years ago by Peixe600

Didn't occur to me to check GEO. Doesn't seem to have any Axiom datasets though

ADD REPLYlink written 6.7 years ago by pufferfish260
0
gravatar for Neilfws
6.7 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Start from the GEO platforms page and search for the SNP array platform of interest. For example "affymetrix snp 6.0".

That query currently returns 3 platforms. One of these is GPL6801. This links to 178 datasets (GEO series) and 10 735 samples. Many of those series have supplementary CEL file data available.

ADD COMMENTlink written 6.7 years ago by Neilfws48k

That data is SNP6, not Axiom

ADD REPLYlink written 6.7 years ago by pufferfish260
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