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Uploading your Sample Manifest to Gencove

  • Updated


After completing your sample manifest, the next step is to upload it directly to the corresponding project within your Gencove account. This ensures:

  • Your manifest and sample IDs are formatted correctly.
  • Restriction of sample identifiers ("client IDs") to those specified in the manifest, helping to prevent the addition of incorrectly named samples. This feature is activated when sample manifest files are uploaded to a project; otherwise, client IDs adhere to Gencove's standard naming practices.

Sample manifests can be attached to a project via the web UI, CLI, or API. When you upload a sample manifest, a notification is sent directly to the Gencove team. 

 

Defining a sample manifest

Sample manifests can be provided in either comma-delimited files (CSV) or Excel files (XLSX). When submitting Excel files, multiple sheets are permissible, with each sheet undergoing validation to ensure correct well formatting (if plates are being sent) and absence of duplicate IDs. We support 3 different manifest formats 1) 96-well, 2) 384-well, 3) tube. When using the tube format, any number of rows can be populated.

While the sample manifest must include all required columns for your project, our tool only mandates populating the Unique Sample Identifier and Well columns for acceptance. This simplifies the upload process across all project types.

  • Plate ID (optional)
  • Well (required)
  • Unique sample identifier (required)
  • Buffer (optional)
  • Concentration (optional)
  • Species (optional)
  • Coverage (optional)

Unique sample identifier column values must meet the following criteria to be valid:

  • Unique in sample manifest (no duplicates). The following special values are exempted from this check: Control, Negative Control, NTC, NC
  • Contain only alphanumeric characters 

When submitting an Excel manifest, all of the above rules apply to each individual sheet. However, note that the Unique sample identifier duplicate check is done against the combination of all sample identifiers across all sheets.

 

Adding a sample manifest through the web UI

 

  1. First you will need to log into your Gencove account.
  2. Under the project detail page, users can click the "Manage sample manifests" section to view the manifest management page.
  3. From the manifest management page, new sample manifests can be uploaded via the "Upload sample manifest" button. This will open a dialog where the user is prompted to upload a manifest CSV or XLSX file.
  4. Once a manifest has been added, it is validated before being registered in the project. If there are any errors with the manifest, they will be listed and the upload will be prevented.
  5. Once a sample manifests have been uploaded, they can be viewed and downloaded at any time from the sample manifests management page.

Managing manifests using the CLI

Project sample manifests can be retrieved or uploaded via the CLI. The following commands can be used:

  • gencove projects create-sample-manifest <project_id> <sample_manifest_path>
    • Upload a sample manifest CSV or XLSX to a target project ID
  • gencove projects get-sample-manifests <project_id> <destination>
    • Download all sample manifests for a project ID to the supplied destination directory
  • gencove sample-manifests get-sample-manifest <manifest_id> <destination>
    • Download a specific sample manifest by ID to the supplied destination directory

 

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