Automatically transfer Torrent Suite™ Software output to Ion Reporter™ Software

To transfer output files from a Torrent Suite™ Software analysis to Ion Reporter™ Software automatically, configure the IonReporterUploader plugin when you create a Planned Run.

The results files that are transferred to Ion Reporter™ Software can be:

  • Automatically defined as samples Ion Reporter™ Software that are launched in an analysis workflow immediately after the instrument run is complete. Successful analyses are then available in Ion Reporter™ Software when you sign in with the account that is included in the setup.

    IMPORTANT! To set up automatic transfer, you must select the IonReporterUploader plugin and select the Ion Reporter™ Software analysis workflow in the Planned Run.

  • Made available in Ion Reporter™ Software as output files (BAM and VCF files) that can later be defined as samples in Ion Reporter™ Software. In this case, you can define your samples and then launch the analysis manually in Ion Reporter™ Software. This approach is commonly used to annotate the VCF files, using the annotation-only analysis workflow in Ion Reporter™ Software.

    VCF files are available as output files when you configure the IonReporterUploader plugin. For details, see Variant calls in Torrent Suite Software.

For sequencing runs that use barcoded data, select the correct barcode kit under Kits in the workflow bar. When you select a barcode kit, a sample name field for each barcode is generated.

Use the plan by Sample Set feature when you configure Ion Reporter™ Software in your Planned Run or template. For details, see Plan by Sample Set.

  1. In the Plan tab, click Templates, then select a Research Application, for example, AmpliSeq DNA.
  2. Select a template that matches your panel.

    For example, if you are using an Ion AmpliSeq™ Exome Panel, select the Ion AmpliSeq™ DNA template with the same name.

  3. Add samples, confirm the default settings, enter a plan name, then select Ion Reporter in the workflow bar.
  4. Select the Ion Reporter™ Software account that you want to use by default for the transfer of output files to Ion Reporter™ Software.

    Data files are transferred to the default Ion Reporter™ Software account, unless you change it during run planning.

    IMPORTANT! If you select None, you must transfer files from Torrent Suite™ Software manually to Ion Reporter™ Software.

  5. If the Ion Reporter™ Software account is not configured, click Configure to add an account.

    For more information, see Set up an account for IonReporterUploader plugin.

  6. Select a Sample Grouping that corresponds to the sample relationship in Ion Reporter™ Software.

    When you select a Sample Grouping, the workflow bar in Ion Reporter™ Software displays only analysis workflows that match the type of analysis workflows selected.

  7. Select an option in the Existing Workflow menu.

    Option

    Description

    Ion Reporter workflow for your sample type

    Use this option to launch automatically the analysis workflow in Ion Reporter™ Software with the sample data from the run. Successful analyses are available in Ion Reporter™ Software with the account and organization that you selected.

    Upload Only

    Use this option to transfer only the output files from the sequencing run to Ion Reporter™ Software. If you use this option, you can access the samples in Ion Reporter™ Software. VCF files are also available if you ran the variantCaller plugin.

  8. (Optional) Click Create New Workflow to open Ion Reporter™ Software in a new browser window. In Ion Reporter™ Software, create your new analysis workflow, then save it.

    When you return to Torrent Suite™ Software, refresh your browser. You can select the newly created analysis workflow in the Existing Workflow menu.

  9. Select an Ion Reporter Upload Option.

    Option

    Description

    Review results after run completion, then upload to Ion Reporter

    Use this option to review the completed run report and then manually transfer the data files to Ion Reporter™ Software.

    IMPORTANT! After you review the results in Completed Runs & Results, you must click Upload to IR > Upload as Planned to upload the data to Ion Reporter™ Software.

    Automatically upload to Ion Reporter after run completion

    Use this option to upload automatically results to Ion Reporter™ Software. If you select an analysis workflow, an Ion Reporter™ Software analysis is launched immediately after the run. Successful analyses are then available in Ion Reporter™ Software when you sign in with the account that is included in the setup.

  10. Continue with the steps to create the Planned Run.

    For more information, see Steps in the workflow bar.

  11. If appropriate, enter the gender of a sample.

    For more information, see Sample gender.

  12. To save the Planned Run or Planned Run template, do one of the following actions in the workflow bar:

    • Click Save for a new Planned Run template, enter the new template name, and optionally mark it as a favorite.

    • Click Save & Finish if you used Plan by Sample Set, then enter the new Planned Run name.

    • Click Plan Run for a new Planned Run, then enter the new run plan name and sample information.

  13. The Planned Run is ready to run on your sequencing system.
Related Topics
Parent topic: Integration with Ion Reporter™ Software
Child Topics
Manage the Ion Reporter™ Software analysis workflow list
Sample gender