• Not able to view data for all chromosomes on IGV

  • Former User of DNAx Community_73
  • 13 June 2022 00:00
  • 0 votes
  • 2 comments

• Multiple job failures + data retention

  • Former User of DNAx Community_69
  • 10 June 2022 00:00
  • 0 votes
  • 4 comments

• Webinar July 14: Analyzing the UK Biobank Dataset with RStudio Workbench

  • Brenton Pyle
  • 10 June 2022 00:00
  • 0 votes
  • 1 comment

• Best strategy for annotating and filtering VCF files using VEP on UKB RAP?

  • Former User of DNAx Community_4
  • 10 June 2022 00:00
  • 0 votes
  • 1 comment

• Have questions about the 200k WGS Joint Variant Call Data Release? Ask them here!

  • Brenton Pyle
  • 08 June 2022 00:00
  • 0 votes
  • 24 comments

• I see that the variants in 450k_OQFE.annotations file are annotated using SNPeff, however there are no inframe deletions or insertions among the annotations. Are they filtered out, if so why? There are only LoF, synonymous and 3 categories of missense.

  • Former User of DNAx Community_45
  • 07 June 2022 00:00
  • 0 votes
  • 1 comment

• New 200k WGS Joint Variant Call Data Release

  • Brenton Pyle
  • 07 June 2022 00:00
  • 0 votes
  • 1 comment

• If I do not see the BIM, MAP, FAM files on my approved database, does this mean that I do not have access to genotype results of chromosomes 1-22?

  • Former User of DNAx Community_91
  • 05 June 2022 00:00
  • 0 votes
  • 2 comments

• 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
  • 02 June 2022 00:00
  • 0 votes
  • 7 comments

• What about something as simple as retrieving the file names (i.e., as would be done with ls or find). Do these also need to be sent through a dx run request? What about visualizing the output (i.e., cat, less..)?

  • Brenton Pyle
  • 01 June 2022 00:00
  • 0 votes
  • 1 comment

• What is the typical time taken to launch a JupyterLab instance? My regular instance (not Spark) has been in "Launching" state for the last 16 minutes. This seems like an excessive amount of time taken to launch. How long does this typically take?

  • Former User of DNAx Community_70
  • 01 June 2022 00:00
  • 1 vote
  • 2 comments

• Will OCT Converter be implemented in the future? i.e the OCT iamges are *.FDS and *.FDA files

  • Brenton Pyle
  • 31 May 2022 00:00
  • 0 votes
  • 1 comment

• Questions about data in gp_scripts table from UKB

  • Former User of DNAx Community_62
  • 26 May 2022 00:00
  • 0 votes
  • 2 comments

• How to export a matrix table as a VCF file after annotation on UKB RAP using HAIL?

  • Former User of DNAx Community_4
  • 26 May 2022 00:00
  • 0 votes
  • 1 comment

• Is ?project? the literal name of this particular project, or it would be ?project? regardless of the actual project name?

  • Brenton Pyle
  • 26 May 2022 00:00
  • 0 votes
  • 1 comment

• Is it useful to convert .nii.gz files to .nii - and what is the difference between the two formats?

  • Brenton Pyle
  • 25 May 2022 00:00
  • 0 votes
  • 1 comment

• Would someone with RAP experience working on annotating VCF files for loss-of-function variants be willing to connect and offer tips/advice? I am new to the field and am feeling rather overwhelmed!

  • Permanently deleted user
  • 24 May 2022 00:00
  • 0 votes
  • 1 comment

• Reading data into RStudio on DNA Nexus

  • Former User of DNAx Community_63
  • 24 May 2022 00:00
  • 0 votes
  • 9 comments

• Do the multiple jobs run simultaneously by default? or does the for loop run everything sequentially?

  • Brenton Pyle
  • 23 May 2022 00:00
  • 0 votes
  • 1 comment

• We are interested in exploring the raw accelerometry data (p90001) from physical activity measurements. This data exists inside 'Bulk' folder within our project as files with '.cwa' file extension. How can we open these '.cwa' files in UK-RAP platform?

  • Former User of DNAx Community_96
  • 23 May 2022 00:00
  • 0 votes
  • 2 comments

• How to store large genotype/phenotype data on the RAP that will be queried within custom code?

  • Former User of DNAx Community_21
  • 20 May 2022 00:00
  • 0 votes
  • 1 comment

• Do you have visualizations for repeated IDPs - trajectories?

  • Brenton Pyle
  • 20 May 2022 00:00
  • 0 votes
  • 1 comment

• Making PHESANT compatible dataset from participant table

  • Former User of DNAx Community_65
  • 20 May 2022 00:00
  • 0 votes
  • 2 comments

• If you want to run commands on many large files (such as whole-genome sequencing CRAM files), won't transferring the files to project storage take a lot of time/compute?

  • Brenton Pyle
  • 19 May 2022 00:00
  • 0 votes
  • 1 comment

• JupyterLab Spark SQL queries keep hanging

  • Former User of DNAx Community_62
  • 19 May 2022 00:00
  • 0 votes
  • 3 comments

• 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
  • 19 May 2022 00:00
  • 0 votes
  • 3 comments

• In the Swiss Army Knife -iin parameter you can specify a whole folder, or do you need to list every single file one by one?

  • Brenton Pyle
  • 19 May 2022 00:00
  • 0 votes
  • 1 comment

• UK Biobank Project Data Update Clarification

  • Permanently deleted user
  • 17 May 2022 00:00
  • 0 votes
  • 1 comment

• Is there an updated version of plink available with the Swiss Army Knife?

  • Former User of DNAx Community_55
  • 17 May 2022 00:00
  • 0 votes
  • 2 comments

• For the chunked population wide 450k WES vcfs, where can one find a position file delimiting the start and end positions of each chunk?

  • Former User of DNAx Community_53
  • 17 May 2022 00:00
  • 0 votes
  • 9 comments

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