Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Are we talking about this notebook? https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/MatrixTable_variant_annotation_with_VEP.ipynb If so, dnax database behaves as a normal Hail Spark o...
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Hi @Chinonso Odebeatu?, this is great timing, I just posted Query of the week #1 which deals with this very topic. Feel free to join me/Community in this discussion. https://community.dnanexus.com/...
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What is the command/analysis you executed?
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I would not expect azure in the list. Are you using UKB-RAP (https://ukbiobank.dnanexus.com/landing) or DNAnexus platform (https://platform.dnanexus.com/login)?
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UKB-RAP is powered by Amazon Web Services (AWS). Azure instances are not available.https://www.ukbiobank.ac.uk/enable-your-research/research-analysis-platform
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Hi @Chinonso Odebeatu?, yes, the Table Exporter should export all the data from your cohort, not just 30k max. For Table Exporter, I normally define the columns to be exported (and I do not try to ...
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Hi Delnaz, Please see my ideas below. When working with the JupyterLab, there are two different filesystems where you can create/open/manage the notebooks. You can either directly work with a noteb...
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a) samtools view is part of Swiss Army Knife (samtools command is specified via -icmd parameter) https://ukbiobank.dnanexus.com/app/swiss-army-knife b) if needed, you can run SAK from your custom m...
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Are you trying 'ls -l /mnt/project/' from JupyterLab or your custom-made applet? If the latter, I would guess that dxfuse is not available.
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In all cases of using dxfuse, it is only performant with sequential (streaming) reads in order, therefore I think that "samtools view /mnt/project/MyBam/test.cram" might be a good use case for dxfu...
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