[Transferring genotype data to an EuroHPC facility] I am wondering if it is feasible to use high-performance computing clusters in Europe, such as LUMI, to analyze the UK Biobank data.
I am writing to inquire about the possibility of transferring genotype data to an EuroHPC facility, specifically the LUMI in Finland. I am wondering if it is feasible to use high-performance computing clusters in Europe, such as LUMI, to analyze the UK Biobank molecular data, provided that all necessary safety and security measures are implemented to ensure data protection and compliance with relevant regulations.
I would be grateful if you could provide me with some guidance on this matter or direct me to the relevant resources to find more information. Specifically, I would like to know if you have any experience in transferring genotype data to HPC clusters in Europe and if there are any processes that need to be followed to make this possible.
Thank you in advance for your time and assistance.
Best,
Vittorio
If researchers do not have student or LMIC applications, they are permitted to download the genotyping data. They need to satisfy themselves that they fulfill the data security requirements of their MTA, in addition to the third-party processor agreement.
If they have a student or LMIC application, download is not permitted and data must be analysed in the RAP.
Please note that the Whole Exome Sequence and Whole Genome Sequence data must not be extracted from the RAP, and must be processed in situ.
Genotyping data may be downloaded via Showcase/AMS or from the RAP. For information on downloading genotype data from Showcase, see https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=263 (but note that UKB data is no longer available from the EGA).
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What is the genotype data you plan to transfer over?
If researchers do not have student or LMIC applications, they are permitted to download the genotyping data. They need to satisfy themselves that they fulfill the data security requirements of their MTA, in addition to the third-party processor agreement.
If they have a student or LMIC application, download is not permitted and data must be analysed in the RAP.
Please note that the Whole Exome Sequence and Whole Genome Sequence data must not be extracted from the RAP, and must be processed in situ.
Genotyping data may be downloaded via Showcase/AMS or from the RAP. For information on downloading genotype data from Showcase, see https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=263 (but note that UKB data is no longer available from the EGA).
For downloading bulk files from the RAP, the following dnanexus documentation pages may be useful. https://documentation.dnanexus.com/downloads
https://documentation.dnanexus.com/user/objects/uploading-and-downloading-files/small-sets-of-files/downloading-using-dx
https://documentation.dnanexus.com/user/objects/uploading-and-downloading-files/batch
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