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Useful links to DNAnexus UKB-RAP resources Pinned Featured
- David C
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How to use Plink in RAP
- Former User of DNAx Community_28
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Hi Please, desperately I need help. I knew Data field 23370 relates to VCF files of whole genome sequencing data. I want to discover how many cases are available for malignant melanoma (WGS). I googled a lot but no clear tutorial I fund. Thanks
- Former User of DNAx Community_7
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retrieve_fields function error
- Former User of DNAx Community_19
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I wonder what is the correct date of UK biobank blood sample collection that were analyzed by WGS? The platform has multiple "Date of attending..." not sure which to use to align dates from ICD codes correctly to the date of sample that was sequenced
- Former User of DNAx Community_23
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Is there a way to download WGS data? Could it be preprocessed on RAP then downloaded if direct download isn't possible?
- Former User of DNAx Community_6
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How to properly write paths with the CLI and dx?
- Former User of DNAx Community_18
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How to tell that a job has failed due to an out of memory error when it completes with state "done"
- Former User of DNAx Community_47
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Issue accessing hail-generated output
- Former User of DNAx Community_6
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I have joined just today I think I should use Cohort Browser to access and analyse any data type. But, I do not have any clue where is the Cohort Browser tab or link (page). I need to access to cancer WGS (or WES) let's say vcf or BAM (CRAM), any help?
- Former User of DNAx Community_8
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Is it possible to include multiple bash scripts in a single applet?
- Former User of DNAx Community_10
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How can I get the protein field names for all 2923 proteins in the new Olink dataset?
- Former User of DNAx Community_9
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Version of the Annotation Database when running the snpEff tool
- Former User of DNAx Community_35
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Is there a way to access locally stored files in project from a submitted job without having to use "dx download"
- Former User of DNAx Community_14
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How to run an applet with a different machine?
- Former User of DNAx Community_10
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I would like to export a list of EIDs of people taking a specific medication list, e.g. aspirin and/or ibuprofen. What is the easiest way to do so from the platform please? And could I look both at gp scripts and also at questionnaire data?
- Former User of DNAx Community_81
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Polite inquiry about how to obtain the specific behavior pattern variables of accelerometry, such as the maximum daily sedentary bout length or the number of daily sedentary bouts?
- Former User of DNAx Community_75
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Does requesting access to the 1km grid coordinate data preclude access to the 100m grid coordinate data?
- Former User of DNAx Community_12
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where does the predictions of incident cases of various disease come from?
- Former User of DNAx Community_12
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Issue stopping the dispensing option
- Former User of DNAx Community_6
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New Data release on UKB-RAP: WGS Data from 500,000 Participants, Proteomics Data & Updated Imaging Data
- Brenton Pyle
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What is the latest status on the UKB data dispensal and refresh.? https://status.dnanexus.com/ shows that the platform upgrade supposed to be completed by November 20 and projects can be refreshed after that date.
- Former User of DNAx Community_72
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How can I get the processing date for alle the 2923 proteins?
- Former User of DNAx Community_56
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I am getting the following error when I try to run these lines in JupyterHub. Any help would be appreciated. sc = pyspark.SparkContext() spark = pyspark.sql.SparkSession(sc) RuntimeError: Java gateway process exited before sending its port number
- Former User of DNAx Community_11
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How long it takes to obtain access to the returned data via RAP? What is the procedure of applying for 100m/1km resolution grid data ?
- Former User of DNAx Community_12
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How to log all command outputs to the log file?
- Former User of DNAx Community_10
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How to view the job_error.json?
- Former User of DNAx Community_10
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