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
│   ├── filtered_feature_bc_matrix              1
│   │   ├── barcodes.tsv.gz
│   │   ├── features.tsv.gz
│   │   └── matrix.mtx.gz
│   ├── filtered_peaks_bc_matrix                2
│   │   ├── barcodes.tsv.gz
│   │   ├── features.tsv.gz
│   │   └── matrix.mtx.gz
│   ├── raw_feature_bc_matrix                   3
│   │   ├── barcodes.tsv.gz
│   │   ├── features.tsv.gz
│   │   └── matrix.mtx.gz
│   ├── raw_peaks_bc_matrix                     4
│   │   ├── barcodes.tsv.gz
│   │   ├── features.tsv.gz
│   │   └── matrix.mtx.gz
│   ├── demo_A_fragments.tsv.gz                 5
│   ├── demo_A_fragments.tsv.gz.tbi             6
│   ├── demo_A_mem_pe_Sort.bam                  7
│   ├── demo_A_peaks.bed                        8
│   ├── demo_E_SortedByName.bam                 9
│   ├── demo.rds                                10
│   ├── demo_report.html                        11
│   └── demo_summary.csv                        12
└── analysis

  1. Transcriptome cell sparse matrix

  2. ATAC cell sparse matrix

  3. Transcriptome raw sparse matrix

  4. ATAC raw sparse matrix

  5. ATAC per fragment information file

  6. Fragments file index

  7. The bam file of ATAC libiary

  8. ATAC peaks

  9. The bam file of RNA libiary

  10. Matrix in rds format

  11. Final report in html

  12. Quality control information in csv