Create a Local Planned Run

To create a sequencing run locally, use the run planning interface on the MiSeq i100 Series Control Software or Illumina Run Manager.

1. Select the menu icon in the upper-left corner.
2. Select Runs.
3. On the Planned tab, select Create run.
4. Enter a run name to identify the run.

The run name can contain a maximum of 255 alphanumeric characters, spaces, periods, dashes, and underscores.

5. [Optional] Enter a description for the run.

The run description cannot contain asterisks (*), brackets ([ ]), or commas (,).

6. Select a secondary analysis
• Local
• None
7. Enter the number of cycles performed in each read:

The total number of read cycles and index cycles cannot exceed the number of cycles specified by the reagent kit. The index cycle limit applies to cycles used as an index, not UMI cycles, or trimmed reads.

• Read 1—Enter the number of cycles for Read 1.
• Index 1—Enter the number of cycles for Index Read 1. For a PhiX-only run, enter 0 in both index fields.
• Index 2—Enter the number of cycles for Index Read 2.
• Read 2—Enter the number of cycles for Read 2. This value is typically the same as the Read 1 value.

The number of cycles is determined by the selected sequencing kit configuration. For more details on available sequencing kit configurations, refer to Sequencing Consumables.

8. Select Next.
9. Select your analysis application.
10. [Optional] Enter a description for the configuration.
11. Select your library prep and index adapter kits.
12. Select Next to configure secondary analysis and add the sample information.

For more information, refer to Set Up DRAGEN Secondary Analysis.

You can create a sample sheet template using the local application on the instrument, or in the cloud using BaseSpace Sequence Hub. The sample sheet must be formatted correctly before you import it.

• To create a sample sheet template using one of the local DRAGEN applications on the instrument, refer to the steps in the Set Up DRAGEN Secondary Analysis section and select Export sample sheet in the final step.
• To export a sample sheet from a planned run in BaseSpace Sequence Hub using a template, navigate to the planned run in BaseSpace Sequence Hub and select Export sample sheet.

The dry cartridge serial number can be used for the Library Tube ID field, or the field can be left blank.

Use the following steps to import the sample sheet.

1. Select the menu icon in the upper-left corner.
2. Select Runs.
3. On the Planned run tab, select Import sample sheet, and then open your sample sheet v2 file.
4. After the sample sheet is validated, select Next to review the imported run details.

During review, the imported run details are editable.

5. [Optional] Perform any of the following actions:
• To edit the run settings or configuration settings, select Edit next to the run or configuration.
• To delete a configuration, select Delete next to the configuration, and then select Yes, delete.
6. To save the run, select one of the following options:
• To edit the run details later, select Save as draft.
• To finalize the run details and plan for sequencing, select Save as planned.