Advanced tools and tutorials
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How do I remove intermediate files created during the WDL workflow? I can see that Terra has an option, any approach for DNAnexus? https://support.terra.bio/hc/en-us/articles/360039681632-Saving-storage-costs-by-deleting-Intermediate-files
- Former User of DNAx Community_100
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Is it possible to generate interactive plotly visualizations in the jupyter notebooks on the RAP? I can load the plotly package and can execute the code but I just see a blank where the visualizations should be.
- Former User of DNAx Community_47
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How can I monitor my jobs and get information on how much memory/disk space is being used, which instance was it allocated to, and so on?
- Permanently deleted user
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Rstudio packages: Loading trouble
- Former User of DNAx Community_79
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mitochondrial DNA copy number (CN) estimation--how do I do it?
- Former User of DNAx Community_10
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Issue with exporting 'eid' using Table Exporter
- Former User of DNAx Community_5
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Low scratch storage space when recoding PLINK files to VCF
- Former User of DNAx Community_5
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Is there a way to save locus zoom results generated through locus zoom app into the storage space?
- Former User of DNAx Community_6
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I am trying to run saige and getting this error. Not sure what could be the reason for this. Can you help me out regarding this?
- Former User of DNAx Community_6
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How to automate phenotype data extraction?
- Former User of DNAx Community_5
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There is a tutorial regarding how to use SAIGE (https://documentation.dnanexus.com/science/scientific-guides/saige-gwas-walkthrough), but here it was not mentioned the GATE (https://github.com/weizhou0/GATE#uk-biobank-gwas-results)
- Former User of DNAx Community_19
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What are the tools that can be used in the UKB RAP for variant annotation?
- Permanently deleted user
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Can one run a PBS job script using qsub in UKB RAP? Can it be done in ttyd?
- Former User of DNAx Community_34
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How to do code separation when building python applet
- Former User of DNAx Community_92
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can I use BOLT LMM for my job and how to use it
- Former User of DNAx Community_31
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Latest data refresh deleted previous cohort datasets and breaks custom dashboards
- Former User of DNAx Community_55
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I'm trying to use "dx upload filename --destination "project/path" from my university network but I'm getting errors like: urllib3.exceptions.ProtocolError: ('Connection aborted.', TimeoutError('The write operation timed out')) Is there an outage?
- Former User of DNAx Community_55
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Using VEP with docker, mount a cache located in my UKB project
- Former User of DNAx Community_68
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Hi there, I'm trying to build a python applet and would like to use multiprocessing module to go faster with the 96 core instance option. Is there a code snippet I can steal for this? I tried the basic one with multiprocessing.pool, but got no luck.
- Former User of DNAx Community_92
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How to run the R script faster on UKB RAP?
- Former User of DNAx Community_34
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Query of the week #8: Filtering BGEN file and exporting geno data to Pandas df
- Ondrej Klempir
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Swiss Army Knife not generating outputs (merged .bed file)?
- Former User of DNAx Community_42
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WDL instance type definition
- Permanently deleted user
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How to use more than 100 machines simultaneously
- Former User of DNAx Community_55
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Anyone else seeing Py4JJavaError today when using toPandas()?
- Former User of DNAx Community_12
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Query of the week #7: About linking geno and pheno data
- Ondrej Klempir
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When connecting to a job via SSH, is there any way to manually send a "Done" signal instead of terminating it with dx terminate ?
- Former User of DNAx Community_48
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Has anyone used locus zoom in DNAnexus before?
- Former User of DNAx Community_6
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I am running an anlysis in jupiter notebook and having issues
- Former User of DNAx Community_6
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file paths in WDL json files.
- Former User of DNAx Community_62
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