• How could we merge exome data (GRch38) and genotype data (GRch37) to explore their LD?

  • Former User of DNAx Community_99
  • 15 May 2023 00:00
  • 0 votes
  • 1 comment

• Saige GWAS giving p value/se == 0 for top hits

  • Former User of DNAx Community_6
  • 15 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

• Has anyone faced issues installing the OlinkAnalyze package in R?

  • Former User of DNAx Community_6
  • 09 May 2023 00:00
  • 0 votes
  • 4 comments

• Can the proteomics dataset be used as is or do any additional filters need to be applied? How to check qc of the data.

  • Former User of DNAx Community_6
  • 09 May 2023 00:00
  • 0 votes
  • 6 comments

• How to access extracted phenotypes?

  • Former User of DNAx Community_5
  • 08 May 2023 00:00
  • 0 votes
  • 1 comment

• How to automate phenotype data extraction?

  • Former User of DNAx Community_5
  • 08 May 2023 00:00
  • 0 votes
  • 2 comments

• How to filter snpEff.vcf.gz file on UKB RAP?

  • Permanently deleted user
  • 08 May 2023 00:00
  • 0 votes
  • 7 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

• Can I use Haploview on DNAnexus

  • Former User of DNAx Community_31
  • 05 May 2023 00:00
  • 0 votes
  • 1 comment

• Hi, I recently noticed that some participants have been automatically removed from the UKB dataset when I updated the dataset. However, I have been working with the previous data, and I want to remove these participants from my datasets

  • Former User of DNAx Community_84
  • 04 May 2023 00:00
  • 0 votes
  • 12 comments

• Why there isn't any variant in the VCF file?

  • Permanently deleted user
  • 01 May 2023 00:00
  • 0 votes
  • 4 comments

• What are the tools that can be used in the UKB RAP for variant annotation?

  • Permanently deleted user
  • 01 May 2023 00:00
  • 0 votes
  • 3 comments

• [Transferring genotype data to an EuroHPC facility] I am wondering if it is feasible to use high-performance computing clusters in Europe, such as LUMI, to analyze the UK Biobank data.

  • Former User of DNAx Community_3
  • 27 April 2023 00:00
  • 0 votes
  • 2 comments

• Can one run a PBS job script using qsub in UKB RAP? Can it be done in ttyd?

  • Former User of DNAx Community_34
  • 27 April 2023 00:00
  • 0 votes
  • 8 comments

• How to do code separation when building python applet

  • Former User of DNAx Community_92
  • 26 April 2023 00:00
  • 0 votes
  • 1 comment

• I am trying to download proteomics data in ukbiobank rap. I could able to extract the variable that was noted in the release email. I dont see any values in the file. I tried downloading through data portal but I am not sure if its downloading or not.

  • Former User of DNAx Community_6
  • 26 April 2023 00:00
  • 0 votes
  • 12 comments

• can I use BOLT LMM for my job and how to use it

  • Former User of DNAx Community_31
  • 26 April 2023 00:00
  • 0 votes
  • 8 comments

• Haplotype/LD analysis using TOPMed impute data

  • Former User of DNAx Community_67
  • 26 April 2023 00:00
  • 0 votes
  • 4 comments

• New Data Release on UKB-RAP: Olink Proteomics Data

  • Brenton Pyle
  • 25 April 2023 00:00
  • 0 votes
  • 14 comments

• Working on processing incident events, need help.

  • Former User of DNAx Community_6
  • 24 April 2023 00:00
  • 0 votes
  • 8 comments

• Webinar June 1: Analyzing the UK Biobank Proteomics Data on the UK Biobank Research Analysis Platform

  • Brenton Pyle
  • 21 April 2023 00:00
  • 0 votes
  • 7 comments

• Latest data refresh deleted previous cohort datasets and breaks custom dashboards

  • Former User of DNAx Community_55
  • 21 April 2023 00:00
  • 0 votes
  • 1 comment

• Is there a field for AAscore from GraphTyper?

  • Permanently deleted user
  • 20 April 2023 00:00
  • 0 votes
  • 1 comment

• 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
  • 20 April 2023 00:00
  • 0 votes
  • 1 comment

• Hi, my UK B data on the RAP has been on refreshing for the past two weeks. I was told that an additional variable I requested has been added but I cannot access it due to refreshing showing 0%. what do I do?

  • Former User of DNAx Community_84
  • 18 April 2023 00:00
  • 0 votes
  • 4 comments

• Using VEP with docker, mount a cache located in my UKB project

  • Former User of DNAx Community_68
  • 18 April 2023 00:00
  • 0 votes
  • 2 comments

• 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
  • 18 April 2023 00:00
  • 0 votes
  • 1 comment

• Has the image_file argument been removed from dx run?

  • Former User of DNAx Community_68
  • 17 April 2023 00:00
  • 0 votes
  • 4 comments

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