• 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

• Mapping ICD10 codes from field 41270 via PheWAS R package using createPhenotypes results in only ~1250 phenotypes. Does anyone know how to get ALL the phenotypes in the UKB - but particularly all related to mental disorders?

  • Former User of DNAx Community_66
  • 29 June 2023 00:00
  • 0 votes
  • 4 comments

• How to download NMR metabolomics data?

  • Former User of DNAx Community_44
  • 28 June 2023 00:00
  • 0 votes
  • 6 comments

• Will the bgenix index files be available for the WGS 200k interim, or do we have to create them?

  • Former User of DNAx Community_58
  • 27 June 2023 00:00
  • 0 votes
  • 2 comments

• Does anybody else encounter random read errors when reading imputed genotypes ?

  • Former User of DNAx Community_48
  • 26 June 2023 00:00
  • 0 votes
  • 5 comments

• How can we execute modified applets without creating duplicated data?

  • Former User of DNAx Community_55
  • 21 June 2023 00:00
  • 0 votes
  • 2 comments

• Why do our forum passwords need to be reset every 3 months?

  • Former User of DNAx Community_55
  • 21 June 2023 00:00
  • 0 votes
  • 2 comments

• Is it possible to access returned data on UKB RAP? I have identified the relevant details of the data I'm interested through the publication (return ID, etc.), though I am unable to find the data using Spark.

  • Former User of DNAx Community_33
  • 20 June 2023 00:00
  • 0 votes
  • 1 comment

• I am trying to extract a specific snip from ukb22418_cMT_b0_v2 the mitochondrial hard called chromosome file, The snps are labeled with Affx-, not rs... How do I extract a specific snp, for example Affx-34461959. The usual plink command doesn't work

  • Former User of DNAx Community_10
  • 19 June 2023 00:00
  • 0 votes
  • 2 comments

• Could you please offer the List of Field Names for All Proteins so that we can download all the proteomic data ?

  • Former User of DNAx Community_43
  • 16 June 2023 00:00
  • 0 votes
  • 2 comments

• How can I convert VCF file to tabular data?

  • Permanently deleted user
  • 14 June 2023 00:00
  • 0 votes
  • 17 comments

• I have a question about the "Haplotypes" file (the 0.06TB one - BGEN and BGI). Does this file only contained pruned SNPs after eliminating those in high LD? I am unable to understand how the haplotypes are stored here. Please Help!

  • Former User of DNAx Community_37
  • 14 June 2023 00:00
  • 0 votes
  • 3 comments

• Location for publicly available models and processed data

  • Former User of DNAx Community_64
  • 13 June 2023 00:00
  • 0 votes
  • 4 comments

• Webinar: Dementia and Multimorbidity in Late-Life Disease: Longitudinal and Multimodal Data Science Approaches

  • Brenton Pyle
  • 12 June 2023 00:00
  • 0 votes
  • 4 comments

• Hi everyone, I am running Regenie form the RAP Command line. I got tis error "set file : [ukb23158_500k_OQFE.sets.txt.gz] ERROR: unknown chromosome code in set list file". I am using the files already available on UKBiobank RAP.

  • Former User of DNAx Community_89
  • 09 June 2023 00:00
  • 0 votes
  • 2 comments

• How to improve the disk speed and data transfer speed in UKB RAP VMs

  • Former User of DNAx Community_15
  • 09 June 2023 00:00
  • 0 votes
  • 4 comments

• 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

• incorporate some additional phenotype variables that are not included here: https://github.com/dnanexus/UKB_RAP/blob/main/end_to_end_gwas_phewas/get-phewas-data.ipynb

  • Former User of DNAx Community_42
  • 06 June 2023 00:00
  • 0 votes
  • 6 comments

• Upload permission required in applet

  • Former User of DNAx Community_84
  • 02 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

• Are there any annotated gds files available for ukbiobank?

  • Former User of DNAx Community_6
  • 29 May 2023 00:00
  • 0 votes
  • 2 comments

• I wrote some JAVA code (jar) which I want to run. How do I do it?

  • Former User of DNAx Community_61
  • 26 May 2023 00:00
  • 0 votes
  • 2 comments

• Whats the best way to do simple operations with files while using bash in the RAP?

  • Permanently deleted user
  • 25 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

• PlateID to sample id linker for proteomics data?

  • Former User of DNAx Community_6
  • 22 May 2023 00:00
  • 0 votes
  • 3 comments

• Query regarding 200k wgs dataset bgen vs Plink format files?

  • Former User of DNAx Community_6
  • 22 May 2023 00:00
  • 0 votes
  • 3 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 skip outputs already generated in WDL?

  • Permanently deleted user
  • 19 May 2023 00:00
  • 0 votes
  • 2 comments

Featured posts

• Ongoing closure of the UKB-RAP
• Our new cost calculator helps you plan with confidence
• New resources for using code repositories with UK Biobank
• Useful links to DNAnexus UKB-RAP resources