Plan step in the workflow bar

Use the Plan step in the workflow bar to review the plan and enter or select additional information to complete the Planned Run.

  1. In the Plan step in the workflow bar, enter or select the required information. The available options are different depending on your sequencing application.

    Option

    Description

    Run Plan Name

    (Required)

    Enter a name for the Planned Run.

    Analysis Parameters

    Select Default to accept default analysis parameter settings (recommended).

    Advanced users can customize analysis parameters by selecting Custom and editing appropriate analysis parameters. For more information, see Copy an analysis parameter set.

    Default Reference & Bed Files

    Reference Library

    Select the reference library file appropriate for your sample. Depending on your application, you may have to select separate DNA, RNA, and Fusions reference library files.

    Target Regions

    Select the target regions BED file appropriate for your sample. Depending on your application, you may have to select separate DNA and fusions target regions files.

    Check with your local Field Service Engineer for updates to ensure that the most current files are being used. For BED file installation instructions, see Upload a target regions file.

    Hotspot Regions

    Select the hotspots (BED or VCF) file that is appropriate for your sample.

    For BED file installation instructions, see Upload a hotspots file.

  2. Depending on your application, select the Use same reference & BED files for all chips/barcodes checkbox if you are using the same reference sequences and target regions and hotspots BED files across all of your chips/barcoded samples in the Planned Run. If you are using different reference sequences or BED files for one or more of your chips/barcoded samples, clear the Use same reference & BED files for all chips/barcodes checkbox.
  3. (Optional) For DNA and Fusions application, select the Same sample for DNA and Fusions checkbox when using the same sample for both DNA and Fusions libraries.
  4. Depending on your application, complete the following:

    Option

    Description

    Number of barcodes

    For barcoded samples, enter the number of barcodes to be used in this run, then click to the right of this option.

    Alternatively, click the first barcode, then click , and all subsequent barcodes are numbered from the first barcode value.

    Number of chips

    For non-barcoded samples, enter the number of chips to be used in this run, then click .

    The Samples Table is populated with barcode information or chip number for each sample.

  5. (Optional) Select an option next to the sequencing application (such as Oncology or Pre-implantation Genetic Screening) to populate required sample information into the Samples Table.
  6. Complete the Samples Table.

    • Save the samples table to a CSV file, fill out required sample information, then upload the samples table to populate the Samples Table automatically.

      1. Click Save Samples Table to save the CSV file to your computer.

      2. Edit the CSV file by entering required sample information into the appropriate sample information columns, then save the CSV file to your computer.

      3. Click Load Samples Table, then select an appropriate CSV file containing sample information specific for this Planned Run.

      4. Click Load to populate the Samples Table in Torrent Suite™ Software with sample information that is supplied by the CSV file.

    • Alternatively, manually enter sample information into the Samples Table using the software. The available options are different depending on your sequencing application.

    Table 1.

    Option

    Description

    Barcode

    For barcoded samples, select a barcode.

    Control Type

    (Optional) Click the Control Type column heading to expand the column, then select the control type.

    Sample ID

    (Optional) Enter a sample ID for each sample.

    Sample Description

    (Optional) Enter a sample description for each sample.

    DNA/Fusions

    For DNA and Fusions application, select DNA or Fusions for each sample.

    Reference

    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.

    Annotations

    Click the Annotations column heading to expand the annotation information that is specific for your application (for example, cancer type or Embryo ID), then complete the required information.

    Sample Tube Label

    Scan or enter the barcode of the Ion Chef™ sample tubes to be used in the run.

    Chip Barcode

    Scan or enter the barcode of the Ion Chef™ sample tubes to be used in the run.

    Sample Collection Date

    Enter the date that the blood sample was drawn.

    Sample Receipt Date

    Enter the date that the laboratory received blood sample.

    Ion Reporter workflow

    Select the Ion Reporter™ Software analysis workflow specific for your run. If you do not see your analysis workflow, select the Show All Worklows checkbox in the column heading.

    This option is available if Ion Reporter™ Software is connected.

    Relation

    Select sample relationship group.

    This option is available if Ion Reporter™ Software is connected.

    Gender

    Select Male, Female, or Unknown.

    This option is available if Ion Reporter™ Software is connected.

    IR Set ID

    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.

  7. (Optional) In Add a note, add a note about your Planned Run.
  8. (Optional) If using LIMS metadata, in Add LIMS Meta Data, enter the text that is associated with the Planned Run.
  9. (Optional) In the Monitoring Thresholds pane, adjust Bead Loading (%), Key Signal (1-100), and Usable Sequence (%) minimum thresholds for your Planned Run.

    If monitoring thresholds are not met, the run is still processed and an alert message is shown on the run report after analysis is complete.

  10. When you are finished with your selections, scroll to the bottom of the screen, then click Plan Run.

    The Planned Run is added to the Planned Runs list on the Planned Runs screen.

Related Topics
Parent topic: Steps in the workflow bar