# Input File Example

## Expression Matrix File Format Description

* `st.rds`: Spatial transcriptomics expression matrix as a Seurat object, which must include the **raw expression matrix**, **gene names**, and other information. For details, please refer to [SDAS input data format description](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/sdas_input). For **multiple slices** of spatial transcriptomics data, a custom `slice_key` can be provided (default is 'sampleID'), which is used for plotting (and for batch information in cell2location). If not provided, it is treated as a single slice.
* `st.h5ad`: Spatial transcriptomics expression matrix as an AnnData object, which must include **spatial coordinates** information, and the cell names (cell index) should be consistent with those in `st.rds`, used for spatial heatmap plotting. For details, please refer to [SDAS input data format description](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/sdas_input).

## Gene Chromosome Position File Format Description (Optional)

* `--gene_order_file`: User-defined gene chromosome position information file, which can be generated by [gtf\_to\_position\_file.py](https://github.com/broadinstitute/infercnv/blob/master/scripts/gtf_to_position_file.py).
  * The `--species` parameter specifies the source of the gene\_order\_file for human/mouse, with row names as gene symbols:
    * human: GRCh38.p12- NCBI:GCA\_000001405.27
    * mouse: GRCm38.p6-NCBI:GCA\_000001635.8

| Gene\_symbol | chr | start | end   |
| ------------ | --- | ----- | ----- |
| MIR1302-2HG  | 1   | 29554 | 31109 |
| FAM138A      | 1   | 34554 | 36081 |
| ...          | ... | ...   | ...   |