Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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to 3) There are two basic sets of files on RAP: Bulk (mostly genomics and imaging) and Database object (phenotypic information). Catalog sits here:https://biobank.ndph.ox.ac.uk/showcase/browse.cgi?...
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@Katie Sandford? Which steps have you already tried to implemented your spark+docker applet? Which bioinformatics functionality you would like to implement? When implementing your applet, have yo...
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I tried to apply a couple of filters in Cohort Browser, based on ICD10 codes, e.g.: A) Search for NOT NULL items in Field Type of cancer: ICD10 (https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=4...
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{@005t000000AD9qLAAT}? Did you consider running Spark based JupyterLab in non-interactive mode? https://documentation.dnanexus.com/user/jupyter-notebooks/references#run-notebooks-non-interactively...
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Hi Michael, Were you able to resolve this? If so, please what was the solution? I would use 3, i.e. one master and 2 cluster nodes, but not sure if this can help in this situation.
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Yes, that is exactly what I would do as the next steps. Here is a list of available instance types:https://dnanexus-prod-asg-dnanexusprodassets4d7ed69b-i607e894f3ya.s3.us-east-1.amazonaws.com/image...
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and/or the following lines worked for me (you can select different instance types to use more memory): df = dataset.primary_entity.retrieve_fields(fields=dataset.primary_entity.fields[:],coding_val...
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My friend @Anastazie Sedlakova? was successful with running the export via (https://github.com/dnanexus/UKB_RAP/blob/main/GWAS/gwas-phenotype-samples-qc.ipynb) cont_df = participant.retrieve_field...
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Hello Michael, I think that retrieving all fields for every participants is not the intended use case as there might be a lot of phenotypic columns in table to be exported. I hope you can preview...
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Which field id and data type you work with? Are you working with 21008 "Imputation from genotype (Genomics England)"? Possible issues with the sample files in GEL and TOPMed Impute datasets have be...
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