Advanced tools and tutorials

Saige null model generation giving error when trying to do on the complete dataset
- Former User of DNAx Community_6
- 30 October 2023 00:00
- 0 votes
- 2 comments
Polite inquiry about how to efficiently analyze the huge raw data of accelerometry on RAP?
- Former User of DNAx Community_75
- 27 October 2023 00:00
- 0 votes
- 3 comments
Results of fewer SNPs total after using PJ Greer's scripts for Regenie using Plink genotype calls and final WES.
- Former User of DNAx Community_33
- 24 October 2023 00:00
- 0 votes
- 2 comments
When I create a notebook in JupyterLab from the DNAnexus tab (project storage), I can't open it. Message says its a protected project. Any suggestions? Do I have too always use dx download then?
- Former User of DNAx Community_97
- 19 October 2023 00:00
- 0 votes
- 6 comments
How to skip downloading files that already exist with dx download?
- Former User of DNAx Community_55
- 17 October 2023 00:00
- 0 votes
- 2 comments
Assistance with LMM-BOLT through the Swiss Army Knife platform: Assertion `CompressedSNPBlocks==1' failed.
- Former User of DNAx Community_25
- 17 October 2023 00:00
- 0 votes
- 4 comments
How can we set a retry policy on dx run jobs?
- Former User of DNAx Community_55
- 16 October 2023 00:00
- 0 votes
- 2 comments
Selection of the GFF file version
- Former User of DNAx Community_35
- 12 October 2023 00:00
- 0 votes
- 2 comments
Extract record tables using the dx command line.
- Former User of DNAx Community_60
- 22 September 2023 00:00
- 0 votes
- 7 comments
I having hard time using STATA 18 on Jupyter lab. Any suggestion on how I can do these ? Thank you
- Former User of DNAx Community_38
- 12 September 2023 00:00
- 0 votes
- 1 comment
How do I archive a folder? I know how to archive multiple files, but I want to archive all the files in one directory recursively.
- Former User of DNAx Community_100
- 09 September 2023 00:00
- 0 votes
- 3 comments
Extracting and saving a specific datafield for all participant in Jupyterlab,
- Former User of DNAx Community_59
- 09 September 2023 00:00
- 0 votes
- 3 comments
accessing the database through SQL Spark is not working
- Former User of DNAx Community_6
- 01 September 2023 00:00
- 0 votes
- 3 comments
WDL workflow and bash/R outputs in DNAnexus?
- Permanently deleted user
- 22 August 2023 00:00
- 0 votes
- 2 comments
Is it possible to run Snakemake pipelines on DNAnexus? I'm trying to use DROP () but having many issues running it, any previous code example on Snakemake that works on DNAnexus?
- Former User of DNAx Community_100
- 09 August 2023 00:00
- 1 vote
- 2 comments
Why does dx tools still have a Python2.7 dependency? Following the directions to install does not work because of this.
- Former User of DNAx Community_2
- 21 July 2023 00:00
- 0 votes
- 1 comment
What is the threshold value for Variant Allele Fraction and Reads on the Mutectcaller app?
- Permanently deleted user
- 09 July 2023 00:00
- 0 votes
- 3 comments
Can I filter when convert from BAM to VCF using the Mutectcaller app?
- Permanently deleted user
- 09 July 2023 00:00
- 0 votes
- 1 comment
Can we create our custom JupyterLab image and run it on DNANexus?
- Former User of DNAx Community_36
- 05 July 2023 00:00
- 0 votes
- 1 comment
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
- 01 July 2023 00:00
- 0 votes
- 1 comment
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
- 07 June 2023 00:00
- 0 votes
- 1 comment
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
- 02 June 2023 00:00
- 0 votes
- 1 comment
Rstudio packages: Loading trouble
- Former User of DNAx Community_79
- 30 May 2023 00:00
- 0 votes
- 1 comment
mitochondrial DNA copy number (CN) estimation--how do I do it?
- Former User of DNAx Community_10
- 25 May 2023 00:00
- 0 votes
- 1 comment
Issue with exporting 'eid' using Table Exporter
- Former User of DNAx Community_5
- 24 May 2023 00:00
- 2 votes
- 5 comments
Low scratch storage space when recoding PLINK files to VCF
- Former User of DNAx Community_5
- 20 May 2023 00:00
- 0 votes
- 5 comments
Is there a way to save locus zoom results generated through locus zoom app into the storage space?
- Former User of DNAx Community_6
- 15 May 2023 00:00
- 0 votes
- 2 comments
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
- 12 May 2023 00:00
- 0 votes
- 3 comments
How to automate phenotype data extraction?
- Former User of DNAx Community_5
- 08 May 2023 00:00
- 0 votes
- 2 comments
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
- 06 May 2023 00:00
- 0 votes
- 3 comments

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