Data enquiries
UKB-RAP, Showcase and data baskets
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Why there isn't any variant in the VCF file?
- Permanently deleted user
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[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
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New Data Release on UKB-RAP: Olink Proteomics Data
- Brenton Pyle
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Working on processing incident events, need help.
- Former User of DNAx Community_6
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Is there a field for AAscore from GraphTyper?
- Permanently deleted user
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Is there a way to specify alleles e.g. (C;C) or (T;C) after an RSID in the cohort browser?
- Former User of DNAx Community_58
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Hesin ICD10 digit availability
- Permanently deleted user
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Are the X-chromosome heterozygosity scores available?
- Former User of DNAx Community_21
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Is there a way to determine which instance should be used for a particular application?
- Permanently deleted user
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I want to perform a GWAS using phenotype and genotype data on unrelated individuals (regression). How to add phenotype, genotype, and covariates data for unrelated individuals either in Jupyter lab or Rstudio on RAP to perform my analysis.
- Former User of DNAx Community_34
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dxfuse mounted filesystem eventually fails with "transport endpoint is not connected"
- Former User of DNAx Community_55
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Is there more detailed information about WGS and WES. For example, BGI WGS CRAM files, Whole genome CRAM files. What specific data are contained in these folders. Thanks!
- Former User of DNAx Community_59
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Uploading many small files very slow: Hi all, I'm trying to extract zipped images and re-upload them to the platform. Although small (each slice is around 250kB), the upload times are prohibitively slow. What is your approach?
- Former User of DNAx Community_64
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Selecting SNPs of Interest and Linking These (Selected SNPs) to Rest of Data
- Former User of DNAx Community_83
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May I ask how I should find the specific genetic data I need in WGS and WES compressed data, since it is impossible to open and check, such as regarding Prostate cancer and Thyroid cancer, do I need to apply the tools . Whether there are relevant codes.
- Former User of DNAx Community_59
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Webinar Apr 13: Flexible Variant Annotation on the UK Biobank Research Analysis Platform
- Brenton Pyle
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I'm wondering if it's possible to understand dates of recurrent diseases in Summary Diagnoses of UKB. For example, an individual was diagnosed with lung cancer in 2010. and again diagnosed with lung cancer (same ICD code) in 2017.
- Former User of DNAx Community_19
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We are trying to unzip the MRI task and rest data using jupyterLab. The project directory is read only. home/dnanexus/<my_project>; Is there a way for us to have read write access to a permanent directory. We have a student account.
- Former User of DNAx Community_74
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How can I store files that aren't automatically deleted upon expiration of my Jupyter Notebook session?
- Former User of DNAx Community_97
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I am trying to analyze the copy number variation (CNV) files (field 22431). How can I map the entries to genes/patients?
- Permanently deleted user
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Do you encourage submitting jobs via local CLI or using the RAP CLI? Are the files paths provided the same when using local CLI or the RAP's CLI?
- Alexandra Lee
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Potential issues with imputed data
- Former User of DNAx Community_51
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Is there a way to download phase 1 release and phase 2 release genotype calls separately? Thanks!
- Former User of DNAx Community_75
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Please, I am very new to the platform and still trying to understand a couple of things. How can I download demographic data and some biochemistry data for all participants from the RAP platform? the cohort browser only displays 30,000 items.
- Former User of DNAx Community_84
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May I use the enhanced PRS (Data-Field 26200) in statistical models without calculating by myself?
- Former User of DNAx Community_67
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Is there a codebook available for where data is located throughout the Research Analysis Platform?
- Former User of DNAx Community_52
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I am trying to access the files from MNT/PROJECT but not accessible
- Former User of DNAx Community_6
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Hello! A couple of questions:1) How do I go about getting approved for accessing the cram files (they are restricted), and 2) Are there other options for accessing raw reads (before variants are called) that are aligned to reference for position only?
- Former User of DNAx Community_75
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I have seen a public resource hosted in google cloud and would like to access that information in DNAnexus. Is it possible to access datasets that are in gs:// from DNAnexus?
- Former User of DNAx Community_6
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Is depth/coverage files available for all WES cram samples? (450K)
- Former User of DNAx Community_44
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