> 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/dam-manual-launch.md).

# DAM Manual Launch

### How to Launch a Manual Analysis

After DRAGEN Spatial Transcriptome has been installed on the DRAGEN Server, the user can execute the run script to launch analyses. The run script requires the same inputs as the ICA workflow, which can be viewed by using the `--help` argument. The primary difference between local and cloud execution is that the user must request a presigned URL and then download the map file to the DRAGEN Server in order to provide it to the app.

### Inputs <a href="#inputs" id="inputs"></a>

Input arguments, folders, and files have the same requirements as listed in Analysis Inputs unless otherwise specified.

For more information about the inputs, see the [Analysis Inputs](/dragen-stratamap/dragen-spatial-transcriptome/analysis-inputs.md) page.

The following are a list of standard inputs files and folders.

| **BCL Folder**               | Sequencing run output directory                           | Yes  |
| ---------------------------- | --------------------------------------------------------- | ---- |
| **Sample Sheet**             | CSV file defining samples and settings                    | Yes  |
| **Map File**                 | Map file (.encrypted.json)                                | Yes  |
| **Image Folder**             | OME-TIFF microscopy images                                | No\* |
| **Analysis Config**          | JSON file with analysis parameters                        | No   |
| Genome                       | `mm39` or `hg38` to select one of the prepackaged genomes | No   |
| Custom Genome (Optional)\*\* | Path to custom genome folder                              | No   |

\*Required unless running in imageless mode

\*\*Refer to the [Genomes section](/dragen-stratamap/dragen-spatial-transcriptome/analysis-inputs/genome.md) for instructions on creating a custom genome.

### Running an Analysis <a href="#running-an-analysis" id="running-an-analysis"></a>

**Basic Analysis with Images**

The most common workflow includes microscopy images for spatial localization. The following are the minimal set of arguments to include for analysis. For additional information, call\
`./run_DRAGEN_Spatial_Transcriptome.sh --help`

Optional and Advanced arguments are listed in the Advanced Options section.

**Default Required Parameters**

| Argument         | Description                     | Example                    |
| ---------------- | ------------------------------- | -------------------------- |
| `--input-folder` | Path to BCL sequencing folder   | `/data/runs/230101_Run1`   |
| `--samplesheet`  | Path to sample sheet CSV        | `/data/samplesheet.csv`    |
| `--genome`       | Reference genome (mm39 or hg38) | `mm39`                     |
| `--map-file`     | Path to map file                | `/data/map.encrypted.json` |
| `--image-folder` | Path to OME-TIFF images         | `/data/images`             |

#### **Example**

```bash
./run_DRAGEN_Spatial_Transcriptome.sh \
    --input-folder /path/to/bcl/folder \
    --samplesheet /path/to/samplesheet.csv \
    --genome mm39 \
    --map-file /path/to/map.encrypted.json \
    --image-folder /path/to/images \
    --output-dir my_analysis_results \
    --run-name "My_Experiment"
```

### **Imageless Analysis**

For workflows without microscopy images, the application uses the SampleLocator feature to automatically detect sample regions. To run an imageless analysis, configure the run script with the following modifications:

* Add `--run-has-images false` to the `run_DRAGEN_Spatial_Transcriptome.sh` command.
* Do not include the image folder.

#### Example

```bash
./run_DRAGEN_Spatial_Transcriptome.sh \
    --input-folder /path/to/bcl/folder \
    --samplesheet /path/to/samplesheet.csv \
    --genome mm39 \
    --map-file /path/to/map.encrypted.json \
    --run-has-images false \
    --output-dir my_imageless_results \
    --run-name "My_Imageless_Experiment"
```

#### How Imageless Mode Works

SampleLocator analyzes sequencing data against the map file to automatically identify and segment tissue regions without requiring microscopy images.

### Advanced Options

The following are additional input arguments available

| `--grid-bin-size`             | Grid bin size(s) in µm (colon-delimited)     | 10        |
| ----------------------------- | -------------------------------------------- | --------- |
| `--cell-boundary-expansion`   | Cell boundary expansion distance in µm       | 5         |
| `--include-introns`           | Include intronic reads in analysis           | false     |
| `--output-bam`                | Output BAM alignment file                    | false     |
| `--output-nuclei-bin-results` | Output nuclei-binned results                 | false     |
| `--analysis-config`           | Path to analysis configuration JSON          | None      |
| `--run-has-images`            | Whether images are included                  | true      |
| `--output-dir`                | Output directory name                        | workspace |
| `--ext-segmentation-folder`   | Absolute path to externalsegmentation folder | None      |
| `--run-name`                  | Run name for run level reports               | None      |
| `--include-introns`           | Include intronic reads                       | false     |
| `--resource-size`             | Resource Size Profile: M, L, XL              | L         |
| `--help`                      | Print help message                           | None      |
| `--dry-run`                   | Create DAM payload, do not execute           | None      |

**Example: Multiple bin sizes with introns**

```bash
./run_DRAGEN_Spatial_Transcriptome.sh \
    --input-folder /path/to/bcl/folder \
    --samplesheet /path/to/samplesheet.csv \
    --genome hg38 \
    --map-file /path/to/map.encrypted.json \
    --image-folder /path/to/images \
    --grid-bin-size "5:10:20" \
    --include-introns \
    --output-dir my_results
```

### Outputs

Refer to the DRAGEN Spatial Transcriptome [Outputs section](/dragen-stratamap/dragen-spatial-transcriptome/outputs.md) for output information:

### **DAM Application Specific Log Files**

| `nextflow.log`    | Output directory root | Main workflow execution log |
| ----------------- | --------------------- | --------------------------- |
| `DAM_startup.log` | Output directory root | Application startup log     |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://help.connected.illumina.com/dragen-stratamap/dragen-spatial-transcriptome/run-setup/dam-manual-launch.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.