Start a Manual Run

Use the following instructions to create a manual run.

1. If you are not signed in, enter your user name and password, and then select Sign In.
2. Select Start.
3. Select an instrument side to perform the run on.
4. At the top of the runs list, select Manual to switch to manual run entry.

Unless configured differently in instrument settings, planned is the default value. For more information, refer to Customize System Settings.

5. If you are performing local secondary analysis for the manual run, do as follows.
a. For run type, select Import sample sheet for local analysis.
b. Select Select and open your sample sheet v2 file.

The selected sample sheet must be in v2 formatting. For information on sample sheet v2 formatting and requirements, refer to the Sample Sheet v2 Resource.

c. Proceed to step 7
6. If you are not performing local secondary analysis for the manual run, do as follows.
a. For run type, select Manual run (generate BCLs only).
b. Enter a run name.

The run name can contain a maximum of 225 alphanumeric characters, spaces, dashes, and underscores.

c. Select single or paired-end for the read type.
d. 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.

• Read 1—Enter the number of cycles for Read 1.
• Index 1—Enter the length of the index read for Index 1. For a PhiX-only run, enter 0 in both index fields.
• Index 2—Enter the length of the index read for Index 2.
• Read 2—Enter the number of cycles for Read 2. This value is typically the same as the Read 1 value.
e. [Optional] Select your sample sheet.

The selected sample sheet must be in v2 formatting. For information on sample sheet v2 formatting and requirements, refer to the Sample Sheet v2 Resource.

7. Select Review, and then review your run.
8. [Optional] If your instrument is connected to the cloud, select a cloud run setting.
9. Select your output folder.

You can change the default output folder in system settings. Refer to Specify the Default Output Folder Location for more information.

10. [Optional] Select a custom recipe file.

If using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit or the Illumina Stranded mRNA Prep kit, selecting the custom recipe is required. Refer to Dark Cycle Sequencing for more information.

11. When finished, select Load consumables.