Hello. I am looking to generate a variant to gene table with all of my candidates from a GWAS. I am having so much trouble finding the information I need on how to download this data and run it. I know it says if you have multiple inputs downloading the data and running it yourself is best. However, I cannot find exactly what I need in order to do this and where all the data is located. Is the GitHub what I would do in my own terminal? cause it links to the google storage and looks to be a different way to access data. I am utterly and completely confused and would love if you could point me in a direction of step-by-step instructions. Thanks!
Hi @Melissa_B, and welcome to the Open Targets Community!
Thank you for posting on the Community — I’m sorry that you are having so much trouble with this. We have some documentation on accessing Open Targets Genetics data in our documentation. This page also includes a list of available datasets and their associated schemas.
It sounds like you are trying to access the data downloads for Open Targets Genetics. What would be your preferred way to do this? We make the data available via:
- The EMBL-EBI FTP: databases/opentargets/genetics
- Google BigQuery (public datasets)
- Google Cloud Storage (paywalled)
Alternately, we have a GraphQL API which you can access using your programming language of choice (we have sample scripts available for Python and R).
hi. Thank you for your reply! The EMBL-FTP link does not work. Also, the instructions provided are very limited. I have gone through the website documentation and I don’t find the instructions I need.
Am I able to do a list of variants to assign genes through the GraphQL API? The examples use a specific study ID, but I want to use my own data. Would I just leave that blank?