Getting started with the UKB-RAP
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Jobs trying to retrieve cached results?
- Permanently deleted user
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Why, in my downloaded main data, does UDI 40001-0.0 contain a lot other that ICD10 codes?
- Former User of DNAx Community_99
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Why i do not see and cannot download the project files inside a custom applet?
- Former User of DNAx Community_3
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How many wallets can each user have associated with the RAP? Is there a way to pay in advance certain amount of money towards storage/analysis in the RAP platform? How is this set up with institutions?
- Permanently deleted user
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Rate card vs quote previewed in RAP
- Permanently deleted user
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Do I have to install dx-toolkit in ttyd to interact with platform?
- Chai Fungtammasan
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If I am on Tier3, do I still have to pay to use RAP?
- Chai Fungtammasan
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Data types
- Permanently deleted user
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How to upgrade to most recent version of dx-toolkit?
- Former User of DNAx Community_22
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Downloading or searching job logs -- where are they?
- Former User of DNAx Community_41
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What are the legal requirements for exporting a subset of the variant calls from the WGS or WES in DNAnexus to our internal (not local machine) work environment. Can we export a subset of variant calls to join with the clinical data?
- Former User of DNAx Community_94
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Is it possible to run a high priority app (e.g. ttyd) while many jobs are queued?
- Former User of DNAx Community_47
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How can I terminate all running/waiting jobs?
- Former User of DNAx Community_47
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200K WGS data
- Permanently deleted user
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Getting "Reconnect Your Account to UK Biobank" every time I try to log in to the RAP
- Permanently deleted user
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gzip can't be run in aws:eu-west2?
- Former User of DNAx Community_41
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How to access returned data sets using the cohort browser
- Former User of DNAx Community_48
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When running dx download within an applet does this incur an egress fee? (data downloaded from project applet is running in) Many Thanks, Barney
- Former User of DNAx Community_51
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What is the best way to separate participant IDs by ancestral genetic grouping? Similar to Data-Field 22006 (Genetic ethnic grouping) but for each ancestral group and not just Caucasians.
- Permanently deleted user
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How to create an applet which uses spark and a custom docker image
- Former User of DNAx Community_8
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What is the best way to filter samples to keep only unrelated individuals as well as only one individual from related pairs? I am working with WES pVCF files.
- Permanently deleted user
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Are there commands similar to squeue, scancel in SLURM for batch submitted jobs using dx run on UKB/RAP? Or any scripts available?
- Permanently deleted user
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What is the best way to use git with the DNANexus platform?
- Former User of DNAx Community_57
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How to easily download/mount many input files in a script or the CLI , onto the temporary worker?
- Former User of DNAx Community_12
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When I generate a new file in a JupyterLab notebook and upload it to my project storage, I cannot access that file in the same session, even if I refresh. I get the error that the file does not exist.
- Former User of DNAx Community_13
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For pVCF best practices how do I reference the GRCh38 fasta? The documentation provides: bcftools norm -m - -f <reference> -Oz -o <normVCF> <inputVCF> as the call to use but I do not know how to designate path to grc38.reference.fasta
- Permanently deleted user
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I'm having difficulty install the R package devtools, has anyone else had success installing this package?
- Former User of DNAx Community_13
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Best way to run the same command on all CRAM files?
- Permanently deleted user
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How to use dxFUSE style file paths in Swiss Army Knife?
- Permanently deleted user
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In a workflow, how to not upload intermediate files and only upload the output of the final step?
- Former User of DNAx Community_12
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