> 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.md).
# Run Setup
## Pre-sequencing
Configure your instrument to send runs to BaseSpace Sequence Hub (BSSH) Run Monitoring and Storage. Prepare your sample sheet for sequencing and secondary analysis using the BSSH Run Planning tool and the directions found in the next section: [Run Planning](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/run-planning.md).
## Sequencing
Sequencing can be done on either a NovaSeq 6000 or a NovaSeq X Series system. Runs must be sent to BSSH using Run Monitoring and Storage for analysis.
For each system, a run can be kicked off in two ways: as part of an **"autolaunch"** run and analysis, or independently, in **"manual mode"** for a manually kicked-off analysis after sequencing is complete.
**Per-lane Loading (NovaSeq X Series systems only):** Multiple Illumina Spatial Transcriptome libraries can be sequenced on the same flow cell if libraries are separated into individual lanes. For more information, please refer to the following section: [Per-lane Loading](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/per-lane-loading.md).
## Analysis
#### Autolaunch Analysis
Runs initiated with autolaunch can be tracked through BSSH. Autolaunch is configured by a sample sheet, which is used for sequencing and analysis.
* For NovaSeq 6000, the sample sheet is generated in the BSSH Run Planning tool and transferred manually to the sequencing instrument to start sequencing.
* For the NovaSeq X Series, a planned run can be generated in BSSH and then selected on the instrument.
* Note: If utilizing per-lane loading on the NovaSeq X Series, autolaunch can only be used to launch one library's analysis. The other analysis or analyses will need to be launched manually in ICA. Please refer to the [Per-lane Loading](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/per-lane-loading.md) subsection.
#### Manual Mode Analysis
For a manual launch, sequencing is done independently from analysis. After sequencing, the analysis needs to be manually kicked off in the ICA UI. See the [ICA Manual Launch](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/ica-manual-launch.md) page.
### Run Type Options Explained
* **Autolaunch**
When kicking off an autolaunch run, sequencing will occur and the data will be transferred to the Illumina Connected Analytics (ICA) platform, where analysis will start without additional user intervention. See the [Run Planning](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/run-planning.md) page for step-by-step instructions for autolaunch.
{% hint style="info" %}
Autolaunch is recommended; however, autolaunch will kick off an analysis of **only one library of one flow cell sequencing run at a time.** If you intend to perform an alternate configuration (e.g., combining two flow cell sequencing runs of the same library into one analysis), a manual analysis must be performed.
{% endhint %}
Autolaunch workflow for the NovaSeq X series and the NovaSeq 6000
* **Manual Mode**
If autolaunch is not desired for secondary analysis, launch a manual sequencing run independently, send sequencing runs to BSSH for storage, and initiate the analysis manually through ICA. Manual launch may be desired for alternate configurations—for example, if combining multiple flow cell sequencing runs of the same library into one analysis, or if utilizing per-lane loading for sequencing.
* **NovaSeq X Manual Mode:** Follow the Instrument Product Documentation instructions for starting a manual run (generate BCLs only) with BSSH Run Monitoring and Storage. Though not used for sequencing, a sample sheet is required for ICA Manual Launch of analysis. See the [Run Planning](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/run-planning.md) page for instructions on creating a sample sheet.
Manual Mode workflow for the NovaSeq X Series
* **NovaSeq 6000 Manual Mode:** Configure a sample sheet using the BSSH Run Planning tool, and contact your Illumina representative for instructions on how to use this sample sheet to kick off a manual sequencing run.
Manual Mode workflow for the NovaSeq 6000
* After sequencing on either instrument, see the [ICA Manual Launch](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/ica-manual-launch.md) page for step-by-step instructions for launching an ICA Manual Launch analysis.
### Alternative Run Configurations Examples
### Example alternate run configuration #1: *Combining two sequencing runs in one analysis (using only manual mode)*
This use case applies if you are planning from the beginning to combine two flow cell sequencing runs into one spatial transcriptome analysis. After sequencing, see the [ICA Manual Launch page](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/ica-manual-launch.md) for step-by-step instructions for launching an ICA Manual Launch analysis.
{% hint style="info" %}
***Note:** To combine multiple sequencing runs into a single analysis, sequencing runs **must** be generated from the same library and same slide.*
{% endhint %}
### Example alternate run configuration #2: C*ombining two sequencing runs in one analysis (using autolaunch and manual mode)*
This use case applies if, **after** completing one autolaunch sequencing run analysis, you want to add more sequencing data to the analysis to improve sensitivity. An additional manual sequencing run can be combined with the previously autolaunched sequencing run into one spatial transcriptome analysis. After sequencing, see the [ICA Manual Launch page](/dragen-stratamap/dragen-spatial-transcriptome/run-setup/ica-manual-launch.md) for step-by-step instructions for launching an ICA Manual Launch analysis.
{% hint style="info" %}
***Note:** To combine multiple sequencing runs into a single analysis, sequencing runs **must** be generated from the same library and same slide.*
{% endhint %}
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