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Query of the Week #1: Export Phenotypic Data to a File Pinned Featured
- Ondrej Klempir
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I am wondering if there is any way/software on DNAnexus platform to call somatic mutations on UKB data?
- Former User of DNAx Community_19
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Performing GWAS on RAP using DX toolkit and swiss-army-knife Pinned Featured
- Former User of DNAx Community_28
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Isn't it about time the JupyterLab instance got an overhaul?
- Former User of DNAx Community_50
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Where can I find the BWA Reference Genome Index file?
- Permanently deleted user
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extracting allele combinations at specific SNPs
- Fatemeh Tabassi Mofrad
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Opening a Rstudio session on UKB RAP
- Karine Alcala
- Edited
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How to Access OMOP database of ukbiobank?
- Former User of DNAx Community_6
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How can I convert VCF file to tabular data?
- Permanently deleted user
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Analyzing UK Biobank WES data using SAIGE-GENE+
- Former User of DNAx Community_9
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Using Stata
- Amy Marie Mason
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Extract multiple regions from CRAM with samtools view on the RAP
- Permanently deleted user
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Hi folks! Ask me anything about UKBRAP or bioinformatics in general! Starting in 90 minutes!
- Ben Busby
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Imputing UKB genotypes with HRC
- Former User of DNAx Community_39
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New Data Release on UKB-RAP: Olink Proteomics Data Pinned
- Brenton Pyle
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Is there a way to mount Project/Bucket folders on VM workers directly, like NFS mount?
- Permanently deleted user
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I am trying to figure out how to subset the protein expression dataset to participants that were randomly selected. Is there a field that denotes whether or not a participant with proteomics data is randomly selected vs preselected by the consortium?
- Former User of DNAx Community_33
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How to import a VCF file? File not found error when importing VCF file with Hail
- Former User of DNAx Community_14
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Which RAP tools work natively with the segmentation of the genome into tiny chunks (with no index)
- James Eales
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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
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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
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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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Hi! Question: How to retrieve all fields (from phenotypic data) for a specific sample or list of samples (provided a file for example)?
- Former User of DNAx Community_85
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I have joined just today I think I should use Cohort Browser to access and analyse any data type. But, I do not have any clue where is the Cohort Browser tab or link (page). I need to access to cancer WGS (or WES) let's say vcf or BAM (CRAM), any help?
- Former User of DNAx Community_8
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Is there a way to access locally stored files in project from a submitted job without having to use "dx download"
- Former User of DNAx Community_14
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end_to_end_gwas_phewas/gwas-phenotype-samples-qc.ipynb
- Permanently deleted user
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