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I want to use WES data to perform analysis, but I can't find information on the exome sequencing batch. Second, are there principal components for WES data analysis?
- Former User of DNAx Community_99
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Error when dx download files from RAP
- Former User of DNAx Community_57
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What should the genotype prefix of bgen be for regenie burden test step 2?
- Former User of DNAx Community_52
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Best approach annotating variants with CADD and gnomAD
- Former User of DNAx Community_29
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Table exporter with all fields?
- Former User of DNAx Community_29
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I am having issues starting a jupyter notebook. I could able to see the notebook running in the monitor section but not where we launched the notebook. Can someone help me how to resolve this?
- Former User of DNAx Community_6
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How the vcf files were formatted and how to process the vcf files.
- Former User of DNAx Community_6
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View saved plots in RStudio on RAP?
- Former User of DNAx Community_57
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I am looking for NMR metabolites in UKB RAP phenotypes. I have a few questions: 1.) May I know how many NMR metabolites are in UKB RAP? 2.) Can you help how to find all metabolites? 3.) What QC steps generally were followed?
- Former User of DNAx Community_6
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dxcompile compile errors
- Former User of DNAx Community_51
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Hello, I am trying to generate phenotypes with Time to Events for the survival analysis I want to conduct. Did anyone generate these before if so Please do let me know how to do it. Thank you so much for the help..
- Former User of DNAx Community_6
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SNP IDs in WGS
- Former User of DNAx Community_56
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I am trying to find WGS vcf files. I see individual-level vcf files per sample. Where can I find joined called vcf files for WGS located? Please do let me know how to access those and use them for the extraction of the gene region I am interested in.?
- Former User of DNAx Community_6
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Working with Hail outside of JupyterLab
- Former User of DNAx Community_41
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Efficient ways to use Swiss Army Knife
- Former User of DNAx Community_56
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ConnectionPoolTimeoutException while working in JupyterLab
- Former User of DNAx Community_41
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Tools tab not showing RStudio as an option?
- Former User of DNAx Community_57
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Using PLINK GWAS tool on the RAP generates a text output file with many duplicates. How do I get rid of the duplicates?
- Former User of DNAx Community_10
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When running dx download within an applet does this incur an egress fee? (data downloaded from project applet is running in) Many Thanks, Barney
- Former User of DNAx Community_51
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I used RAP tool to do a PLINK GWAS but results did not include X or XY files, only 22 autosomes. How do I include X and XY chr files.
- Former User of DNAx Community_10
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How can I get data from a DNA Nexus database into another format?
- Former User of DNAx Community_47
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Where does saved data go on a Jupyter spark cluster?
- Former User of DNAx Community_47
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How to submit a large input-json with dx run?
- Former User of DNAx Community_18
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Will there be UKB WGS PLINK bfiles?
- Former User of DNAx Community_4
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Effectively querying genotypes from the Spark genotype table
- Former User of DNAx Community_22
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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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Extract multiple regions from CRAM with samtools view on the RAP
- Permanently deleted user
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Are UKB pVCF wes files truly bgzipped?
- Former User of DNAx Community_22
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ExecutorLostFailure when trying to write a matrix
- Former User of DNAx Community_22
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The sample code to load a VCF file with Hail is failing for me when I try it on a single 6 Gb VCF from the whole genome pVCFs. Can you help me to resolve this error?
- Former User of DNAx Community_47
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