> 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/outputs/results-folder/mtx-files.md).

# MTX Files

* The following outputs are produced for each sample:
  * Raw or un-binned matrix files
  * Grid-binned matrix files
  * Cell-binned matrix files
  * (Optional) Nuclei-binned matrix files

The following three files provide per-bin or per-cell gene expression information in the commonly used Matrix Market (`*.mtx`) format:

* `matrix.mtx.gz`
  * Count of unique molecules for each cell and gene pair, in sparse matrix format.
* `barcodes.tsv.gz`
  * Raw matrix files format: SBC:Y:X
  * Grid-binned format: bin10:Y:X
  * Cell-binned format: cellid:Y:X
  * NOTES:
    * All X and Y positions are reported in microns using the global substrate position.
    * Cell-binned and grid-binned data report the X:Y position of the center of the cell or bin.
* `features.tsv.gz`
  * Gene name and ID for each gene in the matrix.

### What are Matrix Market Files?

Matrix Market (`.mtx`) files are a standard sparse matrix format used in single-cell and spatial transcriptomics to efficiently store large gene expression matrices. The format is particularly efficient because spatial transcriptomics data is sparse (most genes are not expressed in most cells/bins).

### File Structure

A typical Matrix Market output consists of three files:

1. **`matrix.mtx.gz`** - The sparse expression matrix
   * Contains only non-zero values
   * Format: `row_index column_index value`
2. **`features.tsv.gz`** - Gene/feature information
   * One gene per line
   * Typically: `gene_id gene_name feature_type`
3. **`barcodes.tsv.gz`** - Cell, bin, or spatial barcode identifiers
   * One barcode per line
   * Can be spatial barcodes, cell IDs, or spatial bin identifiers

### Matrix Market File Format Example

**matrix.mtx header:**

```
%%MatrixMarket matrix coordinate integer general
%
30000 5000 1500000
1 1 5
1 234 3
2 1 12
...
```

* Line 1: Format specification.
* Line 2: Comment line.
* Line 3: `n_genes n_barcodes n_nonzero_entries`.
* Following lines: `gene_index barcode_index count`.

For help using these files with third-party tools, see [Third Party Tools](/dragen-stratamap/dragen-spatial-transcriptome/outputs/results-folder/third-party.md).


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