Outputs

Author: SeekGene

Time: 2 min

Words: 205 words

Updated: 2026-10-13

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SeekSpace™ Tools

The following is the output directory structure: Each line represents a file or folder, denoted by "├──", and numbers indicate important output files.

./
├── Outs
│   ├── demo_report.html                           1
│   ├── demo_summary.csv                           2
│   ├── demo_aligned_DAPI.png                      3
│   ├── demo_aligned_DAPI_TIMG.png                 4
│   ├── demo_aligned_HE.png (optional)             5
│   ├── demo_aligned_HE_TIMG.png (optional)        6
│   ├── demo_filtered_feature_bc_matrix            7
│   │   ├── barcode.tsv.gz
│   │   ├── feature.tsv.gz
│   │   ├── matrix.tsv.gz   
│   │   └── cell_location.tsv.gz                   8
│   ├── clustering
│   │   └── demo.rds                               9
│   └── clustering_scanpy
│       └── demo.h5ad                              10
└── Analysis
    ├── scRNA-seq_Analysis
    │   ├── step1
    │   ├── step2                                                
    │   │   ├── featureCounts                   
    │   │   │   └── demo_SortedByName.bam      
    │   │   └── STAR                            
    │   │   │   ├── demo_Log.final.out          
    │   │   │   └── demo_SortedByCoordinate.bam  
    │   │   └── step3
    │   │       ├── filtered_feature_bc_matrix          
    │   │       └── raw_feature_bc_matrix                
    ├── Spatial_Positioning
    │   ├── demo_valid_spatial_umis.csv.gz
    │   ├── demo_spatial_umis_cleaned.csv.gz 
    │   └── Tissue_Detection  
    │       └── demo_bc_under_tissue.csv

1. HTML report of the sample.
2. CSV format quality control information of the sample.
3. High-definition DAPI stained image of the sample.
4. Thumbnail DAPI stained image of the sample.
5. High-definition H&E stained image of the sample (optional).
6. Thumbnail H&E stained image of the sample (optional).
7. Cell sparse matrix.
8. Cell spatial coordinate file.
9. Sample results in RDS format.
10. Sample results in h5ad format.