Hello!
A couple of questions:1) How do I go about getting approved for accessing the cram files (they are restricted), and 2) Are there other options for accessing raw reads (before variants are called) that are aligned to reference for position only?
Hi Chai, Thanks for the quick feedback. I'm looking for WGS files. We are in tier 3 and I'm probably just not understanding how the process works. From the main project directory, I can see the CRAM files via
All Projects/PRS - Aug 29, 2022/Bulk/Whole genome sequences/Whole genome CRAM files but when when trying to download a specific file (ie. 1000038_23193_0_0.cram) using dx on my local machine it doesn't work. Is there a specific way to do this? Thanks so much.
I see. The CRAM for WGS data is available, but you would need to analyze them using UKB-RAP rather than downloading them. We block the download to prevent people from violating the MTA with UKB. You can check with you PI for the copy of MTA. It has a clause saying that the WES (except original 200k WES), WGS, and new genomics data (TOPMed and GEL) must not be downloaded or transfer out of UKB RAP.
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1 Can you share more detail? WGS or WES? Field ID? I can see them on platform, so why do you think they are restricted? What tier of access you have?
2 CRAM would be the only option for raw reads info.
Hi Chai, Thanks for the quick feedback. I'm looking for WGS files. We are in tier 3 and I'm probably just not understanding how the process works. From the main project directory, I can see the CRAM files via
All Projects/PRS - Aug 29, 2022/Bulk/Whole genome sequences/Whole genome CRAM files but when when trying to download a specific file (ie. 1000038_23193_0_0.cram) using dx on my local machine it doesn't work. Is there a specific way to do this? Thanks so much.
I see. The CRAM for WGS data is available, but you would need to analyze them using UKB-RAP rather than downloading them. We block the download to prevent people from violating the MTA with UKB. You can check with you PI for the copy of MTA. It has a clause saying that the WES (except original 200k WES), WGS, and new genomics data (TOPMed and GEL) must not be downloaded or transfer out of UKB RAP.
There are several option to analyze this data on UKB RAP. To start with maybe one of interactive workstation like ttyd, Jupyterlab would work. Then you can try to automate it with swiss-army-knife or write your own application. We will have a training at the end of this month: https://hello.dnanexus.com/uk-biobank-research-analysis-platform-overview OR you can check out our video https://www.youtube.com/playlist?list=PLRkZ0Fz-n3Z7Jg0Vz4vudLYnBza4EUGLM how to use UKB-RAP as well.
Ok! I'll try to get to the training and look at those videos. Thanks again for the help and the quick response.
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