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Import from BaseSpace

Sample Import from BaseSpace​

  • Prerequisites​

    Before you begin:

    • You must have an active BaseSpace Sequence Hub account: BaseSpace Sequence Hub account

    • You must have an active Basepair account

    • Ensure you have read access to both the run and the associated project on BaseSpace. (Runs and projects have separate permissions — sharing a run doesn’t automatically share its project.)

    • If you belong to multiple workspaces (personal or group), set the correct active workspace in BaseSpace: https://basespace.illumina.com/dashboard

  • Import Workflow Overview​

    Step 1: Go to “Import From BaseSpace” Page​

    In Basepair, navigate to Data → Import → BaseSpace. import-from-basespace-option

    Step 2: Select a Region​

    Choose the BaseSpace data region (e.g., US, EU) from which you want to import biosamples. select-region

    Step 3: Choose Source​

    You can import biosamples:

    • From Projects, or
    • From Runs select-project select-run

    Step 4: Select Samples​

    You’ll see a list of biosamples (.fastq files).

    • Multiple selection is allowed.
    • You can choose from:
      • Multiple runs within a project
      • Multiple projects
      • A combination of both select-samples

    Step5: Start Import​

    Click “Upload Samples” to begin the import process. upload-samples

    The progress, logs, and status will be visible on the same page. report-page

  • Import possibilities​

    Import Raw Files​

    • Import .bcl (raw data) files
      • At a time .bcl files from only one run can be imported.

    Sample Grouping​

    • Automatic: Groups biosamples based on BaseSpace metadata.
    • Group into Single Sample: Merges multiple biosamples into one sample during import.

    File Formats Supported​

    • FASTQ (biosample-level) — multiple biosamples allowed per import
    • BCL (raw) — only one run at a time

    Note: Importing both .bcl files and biosamples simultaneously is not supported.

  • Data Sharing Notes​

    • Runs and Projects in BaseSpace are independent.
    • Sharing a run does not share its associated project or biosamples.
    • You can share data with collaborators by:
      • Adding collaborators to a workgroup (grants full access)
      • Sharing a project (grants access to all associated data)
      • Sharing a run (grants read-only access to that run only)

    If you only wish to share FASTQ datasets, download and share them manually. Learn more:

  • Further Reading​

    For advanced users or API integrations:

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