Create a Planned Run with multiple Ion Reporter™ Software analysis workflows
You can automatically launch multiple workflows for use with a single sample when you use preinstalled Planned Run templates for use with the Immune Repertoire research application.
- In the Plan tab, click Templates, then select Immune Repertoire from the left navigation menu.
- In the Template Name column of the templates table, click the template name. For example, Ion AmpliSeq™ Immune Repertoire Assay Plus - TCRB for S5. Alternatively, you can click Favorites, then click the template name, if the template is in the favorites list.
The Create Plan workflow bar opens to the Plan step. The Run Plan Name is prepopulated with the template name.
- In the Planned Run Name field, enter a unique name for the Planned Run. Enter other information in the Plan step as required. For more information, see Plan step in the workflow bar.
- Click the Ion Reporter step in the workflow bar, then select the Ion Reporter Account to which output files will be transferred to in Ion Reporter™ Software.
The Ion Reporter™ Software account that is added to the Planned Run is used to view and further analyze the sequencing run results in Ion Reporter™ Software.
If the Ion Reporter™ Software account is not configured, click Configure to add another account. For more information, see Set up an account for IonReporterUploader plugin.
- Select a Sample Grouping that corresponds to the sample relationship in Ion Reporter™ Software.
The Existing Workflow dropdown menu updates to show only Ion Reporter™ Software analysis workflows that are appropriate for the sample.
- Under Ion Reporter Upload Options, select Automatically upload to Ion Reporter after run completion.
Run results are automatically uploaded to Ion Reporter™ Software when a run is complete. When you select multiple analysis workflows, you have the option to use multiple analysis workflows with a single immune repertoire sample.
- In the Existing Workflow dropdown menu, select the Ion Reporter™ Software analysis workflows to use with the sample for automatic launches in Ion Reporter™ Software.
When a sample and analysis workflows are launched in Ion Reporter™ Software, successful analyses are available for the account and organization that you selected.
- (Optional) To create a new analysis workflow, click Create New Workflow to open Ion Reporter™ Software in a new browser window. In Ion Reporter™ Software, create a new analysis workflow, then save it. When you return to Torrent Suite™ Software, refresh the browser. You can then select the newly created analysis workflow in the Existing Workflow list.
- Click Next to continue with the Planned Run creation. The software takes you to the next step in the workflow bar. Use other steps in the workflow bar to enter or change settings if needed. For more information, see Steps in the workflow bar.
- In the Plan step, manually enter sample information into the Samples Table using the software. Use the Ion Reporter workflow option to select multiple analysis workflows for use with a single immune repertoire sample.
- (Optional) Deselect the Show All Workflows checkbox in the column heading to narrow the list of analysis workflows to only the analysis workflows for use with the nucleic acid type for the sample barcode.
- Click the analysis workflow name under Ion Reporter workflow. A dropdown menu lists available analysis workflows under Ion Reporter workflow.
- For each barcode listed in the Samples Table, select one of the options for use to launch multiple analysis workflows with a single immune repertoire sample.
As you make selections, the settings are updated in the Summary pane. You can also use the information in this pane to review the settings that are predefined by the template.
After you select the analysis workflows for use with the Planned Run, the table lists the number of analysis workflows that are selected. - Manually enter other sample information into the Samples Table using the software. The available options are different depending on which research application is used.
Table 2. Samples Table options Item
Selection
For barcoded samples, select a barcode.
(Required)
Select a sample that is a part of the selected sample set or sets.
(Optional) Click the Control Type column heading to expand the column, then select the control type.
For DNA and RNA applications, select DNA or RNA for each sample.
If using different reference and BED files for one or more samples, click the Reference heading to expand the sections. Then select the reference, target regions, and hotspots files for each sample.
Scan or enter the barcode of the Ion Chef™ sample tubes to be used in the run.
Scan or enter the barcode of the Ion Chef™ sample tubes to be used in the run.
Enter the date that the blood sample was drawn. Click the cell, then select a date in the calendar or enter a date with YYYY-MM-DD format.
Enter the date that the laboratory received blood sample. Click the cell, then select a date in the calendar or enter a date with YYYY-MM-DD format.
Ion Reporter workflow[1]
Select the Ion Reporter™ Software analysis workflows for use with the Planned Run. To narrow the list of analysis workflows to only the analysis workflows for use with the immune repertoire analysis, deselect the Show All Workflows checkbox in the column heading.
This option is available only if Ion Reporter™ Software is connected.
Select sample relationship group.
This option is available if Ion Reporter™ Software is connected.
Select Male, Female, or Unknown.
This option is available if Ion Reporter™ Software is connected.
The super population code assignment for a sample, as defined by the human 1000 genomes project ( www.internationalgenome.org/faq/which-populations-are-part-your-study/). The population is relevant to the analysis of samples by the TCRB-LR assay workflow in Ion Reporter™ Software. The TCRB-LR analysis workflow produces a haplotype group assignment for samples having a population attribute of "European".
The name of a mouse strain. Choose from a select number of the most common strains. In Ion Reporter™ Software 5.12, the selected mouse strain will not affect Ion Reporter™ Software analysis workflows.
Set this option to the same value for related samples. After file transfer, in Ion Reporter™ Software, samples with the same IR Set ID are considered related samples and are launched in the same analysis (for example, normal sample and its corresponding tumor sample).
Do not give unrelated samples the same IR Set ID value even if the value is zero or blank.
This option is available if Ion Reporter™ Software is connected.
1 See step 10 in this procedure for more information. - Click Save Samples Table to save changes to the Samples Table.
- When you have completed the selections, review the settings in the Summary pane, then click Plan Run at the bottom of the Plan step.
The Planned Run is added to the list on the Planned Runs screen.
