Question: Good repository for uploading SNP data (from genotyping array) alongside manuscript?
2
gravatar for devenvyas
2.9 years ago by
devenvyas580
Stony Brook
devenvyas580 wrote:

I am closing in on finishing a manuscript on some SNP analyses from an Affymetrix genotyping array data. Most reputable journals (including the main one I am targeting) will demand that I make my SNP data publicly accessible prior to publication.

My first manuscript was on mitochondrial genome sequences, so making that data available was obvious (Genbank). However, where I should upload is not clear to me. The binary Plink (bed, bim, fam) files total to less than 30 MB, so I am not quite sure where they should go.

Any suggestions?

snp • 1.0k views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by devenvyas580

Have you looked at GEO? They apparently support SNP array submissions (e.g. the Affy SNP 6.0 array). Recommendations for human subject data here. Not sure they would accept PLINK binary filesets as-is, but their standard formats would not be too difficult to generate starting from PLINK.

ADD REPLYlink written 2.9 years ago by Ahill1.5k
1
gravatar for Medhat
2.9 years ago by
Medhat8.3k
Texas
Medhat8.3k wrote:

How to Submit to dbSNP
dbSNP accepts variations from any organism except bacteria

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Medhat8.3k

I am looking for a good way to just upload a Plink dataset in one place, so I am not sure that dbSNP would be a good place.

ADD REPLYlink written 2.9 years ago by devenvyas580
0
gravatar for Ahill
2.9 years ago by
Ahill1.5k
United States
Ahill1.5k wrote:

Is this subject-level human SNP data (consented, de-identified?). Are you also reporting phenotypes? EGA (https://www.ebi.ac.uk/ega/submission/array_based) and dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/about.html) accept data from array-based genotyping platforms.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Ahill1.5k
0
gravatar for devenvyas
2.9 years ago by
devenvyas580
Stony Brook
devenvyas580 wrote:

This is de-identified, consented human SNP data. Whole mitochondrial genomes for many of them are already on GenBank. It is purely population genetics stuff. There are no phenotype data, just genotype data.

I was looking at the Data Dryad, but unless the article is in one of the sponsoring journals, they charge for storage.

ADD COMMENTlink written 2.9 years ago by devenvyas580
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