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zjshi / gt-pro

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verify if specific SNP/gene is in database #39

Closed ramiroricardo closed 2 years ago

ramiroricardo commented 3 years ago

Hi all,

How would you search the database to check if specific SNPs/genes are present?

e.g. if one is interested in a specific gene of species X.

Thanks

zjshi commented 2 years ago

I apologize for my long delayed response. GT-Pro has been updated frequently until recently. For a specific SNP, one may look it up with the corresponding variant file (VCF format) and reference genome at https://fileshare.czbiohub.org/s/waXQzQ9PRZPwTdk?path=%2Fvariation_in_species. For a specific gene, additional step (gene prediction) may be required before the lookup. It is typically done with programs like Prodigal with reference genome as input. I am closing this issue for now. Feel free to reopen it if you have follow-up questions.