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  • BaseSpace CLI: downloading project data from individual runs

    We have a MiSeq run that needed to be repeated due to low quality. The repeated run performed well and I want to download the data using BaseSpace CLI.
    The SampleSheet was mostly identical and the repeated samples have the same names and belong to the same project.
    When I download with "bs download project", I get the files from both runs simultaneously, making it rather difficult to separate the "good files" from the "bad files".
    I checked to documentation and the help text of the command but couldn't find an option to include or exclude individual runs from the download.

    Is there a way to download all the FASTQ files of a project from one run?

    Alternatively: is there a way to download the FASTQ files of a single run?
    I have tried "bs download run -i [RUNID] --extension fastq.gz" but only got the error message "nothing to download".

  • #2
    I think your command format is just flipped, bs run download --id <run ID> -o <output path>, not bs download run --id <run ID> -o <output path>

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