> 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/analysis-inputs/analysis-config-file-optional.md).

# Analysis Config File (Optional)

The analysis configuration file is an optional input to the DRAGEN Spatial Transcriptome pipeline. It is a JSON file that specifies parameters for alignment, filtering, normalization, and tertiary analysis.

### Example Analysis Config

```json
{
  "mt_threshold": 50,
  "include_only_uniquely_aligned": false
}
```

### Secondary Analysis Parameters

<table><thead><tr><th width="256">Parameter</th><th width="287">Description</th><th>Default value</th></tr></thead><tbody><tr><td>bin_sizes</td><td>Size of the grid bins used in the analysis, in microns.</td><td>10</td></tr><tr><td>expansion_um</td><td>The cell-border expansion distance, in microns, applied to detected nuclei.</td><td>5</td></tr><tr><td>mitochondrial_chr</td><td>Names used for the mitochondrial chromosome so that mtRNA percentage is calculated correctly. Only required when using a custom genome that does not match any of the default names.</td><td>"chrm,m,mt"</td></tr><tr><td>output_nuclei_bin_results</td><td>Determines whether nuclei-bin results are included in the output.</td><td>false</td></tr><tr><td>include_introns</td><td>Include intronic reads in the analysis.</td><td>false</td></tr><tr><td>include_only_uniquely_aligned</td><td>Include only uniquely aligned reads in the analysis, excluding multimappers.</td><td>false</td></tr><tr><td>mapping_parameters_for_DRAGEN</td><td>Pass any parameter that affects DRAGEN alignment. See below for details.</td><td>None</td></tr></tbody></table>

#### mapping\_parameters\_for\_DRAGEN Explained

To allow for customized analysis parameters in DRAGEN, the pipeline accepts any valid DRAGEN alignment parameter through this argument. For a complete list of options, see the DRAGEN product guide: [here](https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/dna-map-align).

For example, to increase the threshold for an acceptable alignment, you could pass:

```json
{
  "mapping_parameters_for_DRAGEN": "--Aligner.aln-min-score=50"
}
```

To pass more than one argument, separate them with a space in a single JSON entry:

```json
{
  "mapping_parameters_for_DRAGEN": "--Aligner.aln-min-score=50 --Aligner.mismatch-pen=5"
}
```

### Tertiary Analysis Parameters

<table><thead><tr><th width="223.2000732421875">Parameter</th><th width="359">Description</th><th>Default value</th></tr></thead><tbody><tr><td>mt_threshold</td><td>Filters out cell or grid bins with a higher percentage of mitochondrial transcripts than the specified threshold.</td><td>40</td></tr><tr><td>umi_count_threshold<br>or<br>umi_percentile_threshold</td><td><p>Filters out cell or grid bins with fewer unique molecules than the specified count threshold, or below the specified percentile threshold.</p><p><em>Note: These parameters are mutually exclusive. Specify only one.</em></p></td><td>100<br>or<br>5th percentile<br><br>If neither is specified, whichever value is higher is used.</td></tr><tr><td>normalize_target_sum</td><td>Sets the total transcript count for each cell or grid bin so that every cell has the same total count after normalization.</td><td>Median count prior to normalization</td></tr><tr><td>top_n_genes</td><td>Filters out low-variability genes, keeping only the specified number of highest-variability genes.</td><td>3000</td></tr><tr><td>umap_min_dist</td><td>The minimum distance between points in the Uniform Manifold Approximation and Projection (UMAP) embedding. Smaller values preserve local structure better, while larger values emphasize global relationships.</td><td>0.5</td></tr><tr><td>leiden_resolution</td><td>Controls the resolution parameter in Leiden clustering. Higher values typically produce more, smaller clusters, while lower values produce fewer, larger clusters.</td><td>1</td></tr></tbody></table>

### Other Parameters

These parameters should not be used unless explicitly directed by support.

<table><thead><tr><th width="256">Parameter</th><th width="287">Description</th><th>Default value</th></tr></thead><tbody><tr><td>override_cycles</td><td>Override the default sequencing cycles for specific protocols.</td><td>"I30;N22U7Y71;N8"</td></tr><tr><td>override_reads</td><td>Override the default read lengths for specific protocols.</td><td>"I30;Y100;I8"</td></tr></tbody></table>


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