Which SNP is the best to use for GWAS from SNP-seek (IRRI) data set?
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4.2 years ago

I want to do GWAS in rice. There are several SNP data set from 3000 rice accessions provided by IRRI (http://snp-seek.irri.org) i.e: 1. all (32M) 2. base (18M) 3. filtered (4.8M) 4. core (404k) However, I only use 300 accessions from those.

Which data set I should use for genotyping in my GWAS analysis?

SNP SNP-seek GWAS Genotyping • 1.2k views
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This would perhaps be better directed at the IRIC so that you can understand, better, the differences between the different databases (and then decide which is best for your own purposes).

There are not many rice researchers here.

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