Output descriptions

“Here’s the output directory structure: each line represents a file or folder, indicated by “├──”, and the numbers indicate three important output files.

./
├── Outs
│   ├── demo_report.html                           1
│   ├── demo_summary.csv                           2
│   ├── demo_aligned_DAPI.png                      3
│   ├── demo_aligned_HE.png (optional)             4
│   ├── demo_aligned_HE_TIMG.png (optional)        5
│   ├── demo_filtered_feature_bc_matrix            6
│   │   ├── barcode.tsv.gz
│   │   ├── feature.tsv.gz
│   │   ├── matrix.tsv.gz   
│   │   └── cell_location.tsv.gz                   7
│   └── clustering
│       └── demo.rds                               8
└── 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. Final report in html

2. Quality control information in csv

3. Slide image in DAPI staining

4. Slide image in H&E staining(optional)

5. Slide thumbnail in H&E staining(optional)

6. Filtered feature-barcode matrix

7. cell coordinates file

8. matrix in rds format