> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-stratamap/dragen-spatial-transcriptome/run-setup/run-planning.md).

# Run Planning

## How to Create DRAGEN Spatial Transcriptome Runs in the BaseSpace Run Planning Tool

The BaseSpace Sequence Hub (BSSH) Run Planning tool is used to generate a planned run or an exportable sample sheet in v2 format for use on the NovaSeq 6000 and NovaSeq X Series systems, which can kick off an Autolaunch analysis.

The Run Planning tool can also be used to generate a sample sheet for use with ICA Manual Launch. If Autolaunch is not desired for secondary analysis, please see the [ICA Manual Launch](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/ica-manual-launch.md) subsection before continuing.

{% hint style="info" %}
*Optional:* For more information on fields that appear in ICA sample sheets, refer to the [Sample Sheet](/dragen-stratamap/dragen-spatial-transcriptome/analysis-inputs/sample-sheet.md) section of this guide.
{% endhint %}

{% hint style="warning" %}
**Prior to setting up DRAGEN Spatial Transcriptome runs in BSSH Run Planning, ensure that image processing is complete after the Illumina Spatial Image Tool and that sample images have been successfully exported to the selected ICA location and BaseSpace Workgroup.**
{% endhint %}

The sections below represent each step in the BaseSpace Run Planning tool.

## Step 1: Run Settings

Log into BSSH using your Illumina account credentials and select your desired workgroup from the account dropdown menu in the upper right corner of the home screen.

From the home screen, select **Runs**.

Select the **New Run** dropdown menu and select **Run Planning.**

Enter parameters and select **Next** to move forward.

For more details on Run Settings parameters, refer to **Table 1.**

{% hint style="info" %}
**Note:** The NovaSeq X Series run setup configuration is different compared to other instrument platforms and allows for multiple analysis configurations for a planned run. **DRAGEN Spatial Transcriptome is not compatible with other analysis configurations.** When running DRAGEN Spatial Transcriptome on the NovaSeq X Series, enter the appropriate Read 1, Read 2, Index 1, and Index 2 values described in the instructions below, and select DRAGEN Spatial Transcriptome as the **only** Analysis configuration.
{% endhint %}

<figure><img src="/files/urI1PKXiDbpOh1jbLgc8" alt=""><figcaption></figcaption></figure>

**Table 1.** Run Setting Parameters

<table><thead><tr><th width="320">Parameter Name</th><th width="168">Required</th><th>Description</th></tr></thead><tbody><tr><td>Run Name</td><td>Required</td><td>Run Name can contain 255 alphanumeric characters, dashes, underscores, periods, and spaces, and must start with an alphanumeric character, a dash, or an underscore.</td></tr><tr><td>Run Description</td><td>Optional</td><td>Run Description can contain 255 characters except square brackets, asterisks, or commas.</td></tr><tr><td>Instrument Platform</td><td>Required</td><td><p>Choose from the following supported instruments:</p><ul><li>NovaSeq 6000/6000Dx</li><li>NovaSeq X Series</li></ul></td></tr><tr><td>Secondary Analysis</td><td>Required</td><td>Select BaseSpace/Illumina Connected Analytics (to generate a sample sheet for cloud analysis).<br>Local is not supported at this time.</td></tr><tr><td>Read 1</td><td>Required on Instrument Platform NovaSeq X Series</td><td>Fill with value 130 for DRAGEN Spatial Transcriptome analysis.</td></tr><tr><td>Index 1</td><td>Required on Instrument Platform NovaSeq X Series</td><td>Fill with value 8 for DRAGEN Spatial Transcriptome analysis.</td></tr><tr><td>Index 2</td><td>Required on Instrument Platform NovaSeq X Series</td><td>Fill with value 0 for DRAGEN Spatial Transcriptome analysis.</td></tr><tr><td>Read 2</td><td>Required on Instrument Platform NovaSeq X Series</td><td>Fill with value 0 for DRAGEN Spatial Transcriptome analysis.</td></tr><tr><td>Sample Container ID</td><td>Optional</td><td>Unique identifier for the container that holds the sample.</td></tr></tbody></table>

## Step 2: Configuration

{% hint style="info" %}
Note: On the NovaSeq X Series, this page is called "Configuration 1". The right-hand corner of the UI displays the Read 1, Read 2, Index 1, and Index 2 values entered on the previous Run Settings screen.
{% endhint %}

Select **DRAGEN Spatial - 1.0.0** from the dropdown menu in the **Application** section. The library prep kit and index adapter kit will auto-populate based on the application selection.

To move forward, select **Next**.

For more information on Configuration Parameters, see **Table 2.**

<figure><img src="/files/Bph2aIK73uDKKQHj6e5o" alt=""><figcaption></figcaption></figure>

**Table 2.** Configuration Parameters

| Parameter Name    | Required | Description                                              |
| ----------------- | -------- | -------------------------------------------------------- |
| Application       | Required | DRAGEN Spatial Transcriptome v1.0.0                      |
| Description       | Optional | Optional text field                                      |
| Library Prep Kit  | Required | Automatically set to Illumina Spatial Transcriptome Prep |
| Index Adapter Kit | Required | Automatically set to Illumina Spatial Transcriptome Prep |

## Step 3: Import Samples from Illumina Spatial Image Tool

There are two options for importing sample information into the sample sheet for DRAGEN Spatial Transcriptome analysis. You may select "From BSSH files" or "From this computer" if the output from the Spatial Image Tool was exported locally and to cloud at the same time.

{% hint style="info" %}
If the output from the Spatial Image Tool was exported to one location only (local or BSSH), use the corresponding method below to select sample information.
{% endhint %}

Selecting "From BSSH Samples":

1. Select the "Import Samples" button at the top of the samples table.
2. Select "From BSSH files".
3. Within the file selection box, browse or search for the samples file using the Substrate ID of the experiment and press Select.
4. Once imported, the samples will appear in the samples table as well as in the per-sample configuration table at the bottom of the page. Review the samples and image file names to ensure they are correct.

Selecting "From this computer":

1. Select the "Import Samples" button at the top of the samples table.
2. Select "From this computer".
3. Navigate to the location where the "samples\_for\_substrate.csv" file was stored upon local export from the Illumina Spatial Image Tool.
4. Once imported, the samples will appear in the samples table as well as in the per-sample configuration table at the bottom of the page. Review the samples and image file names to ensure they are correct.

{% hint style="info" %}
There will be an expected error after you select and fill in the table with either of the above options. This message can be ignored with no further intervention. To move forward, simply close the message.
{% endhint %}

<figure><img src="/files/5hzyWud2gF8bt7JLyiJm" alt=""><figcaption><p>Screenshot of the expected error message</p></figcaption></figure>

## Step 4: Complete Sample & Analysis Settings

Once samples from the Illumina Spatial Image Tool have been imported, fill out the remaining fields. For additional details, refer to **Table 3**.

**Table 3**. Sample and Analysis Parameters

| Parameter Name                  | Required                                                                                                                                                | Description                                                                                                   |
| ------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------- |
| Read Lengths: Read 1 and Read 2 | Required for NovaSeq 6000. Not applicable on NovaSeq X Series.                                                                                          | Auto-filled with the standard values, but can be optionally overwritten.                                      |
| Lane Usage                      | You may select the checkbox to "Repeat set of samples across all lanes" or select all lanes manually via the dropdown menu within each row of the table | The checkbox allows users to "Repeat set of samples across all lanes".                                        |
| Lanes                           | Required                                                                                                                                                | Specifies lanes for each sample. Select the unmarked checkbox at the top of the dropdown to select all lanes. |
| Project                         | Optional                                                                                                                                                | Optional field to describe the associated project.                                                            |

### Analysis Settings:

Enter Analysis Settings parameters. For more information on parameters, see **Table 4.**

Upon completion of configuring parameters, select **Next** to move forward to Run Review.

**Table 4**. Analysis Settings Parameters

| Setting Name                     | Required | Description                                                                                                                                                                                                                                                                                          |
| -------------------------------- | -------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Reference Genome                 | Required | <p>Selected from the following supported genomes:</p><ul><li>Homo sapiens \[1000 Genomes] hg38 v\*</li><li>Mus Musculus \[UCSC] mm39\*</li></ul><p><em>Note:</em> If you shared a custom genome of interest with an Illumina representative, it will be shown here.</p>                              |
| Grid Bin Size                    | Required | Define the size of grid bins in μm. The recommendation is to use 10μm; the minimum bin size is 5μm. Multiple sizes can be specified using an array of integers delimited by colons, e.g., 5:10:25 for bin sizes 5, 10, and 25 μm. Use of multiple bin sizes will increase computation time and cost. |
| Cell Boundary Expansion Distance | Required | Used in cell segmentation. Sets the cell expansion distance from the cell nucleus, in μm. The recommendation is 5μm.                                                                                                                                                                                 |
| Map Align Output Format          | Required | The recommendation is to keep this set to "None". Generating BAM files will require additional compute and storage costs.                                                                                                                                                                            |

## Step 5: Run Review

Once all details have been entered and pass the system check, the details can be reviewed on the Run Review screen. On this page, details from previous steps can be edited, or the sample sheet can be exported. Select **Export** to export the sample sheet.

<figure><img src="/files/m2kiZSvuGW2Pk0ZkK6Qr" alt=""><figcaption></figcaption></figure>

**For NovaSeq 6000:** After exporting the sample sheet, click "Cancel" to finish run planning.

{% hint style="info" %}
Note: After leaving by selecting "Cancel", the run and sample sheet will not be accessible.
{% endhint %}

**For NovaSeq X Series:** The run can be saved as a draft or as a planned run (via "Save as Draft" or "Save as Planned", respectively). Either selection will save the run to the Planned Runs screen within BSSH.

#### Planned Runs Screen (NovaSeq X Series only) <a href="#planned-runs-screen-novaseq-x-series-only" id="planned-runs-screen-novaseq-x-series-only"></a>

The Planned Runs screen lists all planned or drafted runs. Users can set drafted runs to planned, export the sample sheet, and edit or delete a run on this screen.

Once the run is saved as Planned, it will appear on the NovaSeq X Series instrument, where it can be selected for sequencing.

For more information on run planning, refer to the [BaseSpace Sequence Hub support site page](https://help.basespace.illumina.com/).


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