Getting started with the UKB-RAP
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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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New 200k WGS Joint Variant Call Data Release
- Brenton Pyle
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It seems that the recently dx uploaded files does not show up on /mnt/project until I re-start the whole Jupyter Lab VM
- Brenton Pyle
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Do the multiple jobs run simultaneously by default? or does the for loop run everything sequentially?
- Brenton Pyle
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Do you have visualizations for repeated IDPs - trajectories?
- Brenton Pyle
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How to install the dx toolkit. A question came up in our variant annotation workshop today about how to install the dx toolkit (the command line interface that allows you to interact with the UKBRAP). Heres documentation for that specifically:
- Ben Busby
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Hi, I am new to DNAnexus. I want to create a project. However, I met an error which is "The application is not enabled for RAP". I do have a UKB project and I enter the specific application ID. I wonder if you can help me? Thank you~
- Former User of DNAx Community_83
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Why 0 participants but 416.36TiB of data?
- Former User of DNAx Community_39
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I am a student researcher who is unsure about the financial impact of UKB RAP. Has anyone in a similar situation had any experience applying for enhanced credits and could share if it is easy to apply, and how to gauge if I'm likely to run out of credit?
- Former User of DNAx Community_31
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What cost an almost finish job shifts to wait status and restart?
- Permanently deleted user
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How to define a cohort from a list of EIDs?
- Former User of DNAx Community_26
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Dementia Researcher Roundtable Mar 31: Working with Large-Scale Datasets to Enable Discovery
- Brenton Pyle
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How to suppress job notification emails
- Former User of DNAx Community_61
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Is there a way to mount Project/Bucket folders on VM workers directly, like NFS mount?
- Permanently deleted user
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Just wondering if there is dx commands that is equivalent to: find /path -name "*.bam" that can list all bam files with complete paths under /path directory. If not how about something like ls */*/*.bam? Thanks for help.
- Permanently deleted user
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DXSearchERror encountered when running OpenBio notebook
- Former User of DNAx Community_7
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I am trying to set up ssh settings so I can run a workstation. I am getting the following error when trying to run the command using CLI on a windows workstation. I have installed python version 3 and reinstalled dx CLI. Many thanks for your help!
- Former User of DNAx Community_45
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How can I create a list of all files available in a project in the RAP? Thanks!
- Former User of DNAx Community_93
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What would be the cost of calculating a multilevel linear regression model with categorical exposure , continuous outcome, 15 covariates in the 500.000 particpant dataset including analytical weights and with missing values imputed by chained equations?
- Former User of DNAx Community_41
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How do I specify the field titles for Table Exporter? I want to the export Docosahexanoic Acid field. I have tried specifying this field as 'p23450_i0', 'p23450_i0_a0', and even the human-readable name, but keep getting a 'Field title(s) not found' error.
- Former User of DNAx Community_4
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Are there any RAP grants available to the student researchers with UKB access to run some analysis besides the introductory 40 pounds?
- Former User of DNAx Community_19
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Is anyone on this forum using CWL or WDL workflows? If so, I'd be happy to discuss some tips and tricks for getting them to work on the platform! Cheers! Ben
- Former User of DNAx Community_15
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How do I change my profile settings?
- Former User of DNAx Community_1
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