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Former User of DNAx Community_56

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Recent activity by Former User of DNAx Community_56

  • How can I get the processing date for alle the 2923 proteins?

    Hello,   I have started working with the proteomics data (table 1072, field 30900). I wanted to use the date of processing, but it is only available for 1463 proteins out of 2923. I am uisng the fo...

    • 3 followers
    • 4 comments
    • 0 votes

  • SNP IDs in WGS

    Hello,   I noticed there are many cases of different variants at the same position, such as: 22   chr22:50473781:IG    0    50473781    T    TC 22   chr22:50473781:SG    0    50473781    A    T   ...

    • 3 followers
    • 4 comments
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  • Efficient ways to use Swiss Army Knife

    I have been using the RAP on DNA nexus running analyses on the 150k WGS data. I have mostly been using the Swiss Army Knife tool on the graphic interface to convert vcf to plink files and use thes...

    • 2 followers
    • 2 comments
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  • Saving files created with Rstudio

    Hello, I am running some analyses using R on the platform. I don't seem to be able to save the files that I create. I checked here https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research...

    • 3 followers
    • 5 comments
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  • Parallel analyses on WGS files

    Hello, I need to run parallel analyses on the WGS files for each chromosome, I am using the Swiss Army Knife. There are at least 900 files for each chromosome and it seems that the system crashes f...

    • 2 followers
    • 2 comments
    • 0 votes

  • Hello, 1) are the plink files for the WGS going to be available soon? 2) I need help to run batch jobs on SAK

    I am running the Swiss Army Knife using the GUI. I need to convert a list of files from vcf to plink so I am running the analysis in batch. This is the command I am using:for file in ukb23352_c21_*...

    • 3 followers
    • 4 comments
    • 0 votes

  • How to merge VCF files with Swiss Army Knife?

    I am using Swiss Army knife to merge VCF files with Bcftools. I am using the following command: cmd: bcftools merge -m none --file-list files_to_merge.txt -Oz -o MergedFiles.vcf.gz   The input file...

    • 5 followers
    • 8 comments
    • 0 votes