Outputs

Author: SeekGene

Time: 2 min

Words: 356 words

Updated: 2026-10-13

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SeekArc™ Tools

ARC Multi-omics Analysis Outputs

The main output directory structure for ARC multi-omics analysis is shown below. Each line represents a file or directory, and the numbers indicate important output files. demo is the example sample name.

./
├── 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. Cell-filtered sparse gene expression matrix.
2. Cell-filtered sparse ATAC Peak matrix.
3. Raw sparse gene expression matrix.
4. Raw sparse ATAC Peak matrix.
5. ATAC fragment information file.
6. Fragment file index.
7. ATAC library alignment BAM file.
8. ATAC Peak file.
9. RNA library alignment BAM file.
10. Seurat object and downstream analysis results in RDS format.
11. Analysis report in HTML format.
12. Quality-control statistics in CSV format.

RNA-only Library Analysis Outputs

The main output directory structure for RNA-only library analysis is shown below. demo is the example sample name.

./
├── analysis
│   └── demo_E
│       ├── step1
│       │   ├── demo_E_1.fq.gz
│       │   └── demo_E_2.fq.gz
│       ├── step2
│       │   └── featureCounts
│       │       └── demo_E_SortedByName.bam     1
│       ├── step3
│       │   ├── raw_feature_bc_matrix           2
│       │   │   ├── barcodes.tsv.gz
│       │   │   ├── features.tsv.gz
│       │   │   └── matrix.mtx.gz
│       │   ├── filtered_feature_bc_matrix      3
│       │   │   ├── barcodes.tsv.gz
│       │   │   ├── features.tsv.gz
│       │   │   └── matrix.mtx.gz
│       │   ├── counts.xls
│       │   ├── detail.xls
│       │   └── umi.xls
│       └── step4
│           ├── demo.rds                        4
│           ├── gex_tsne_umi.xls                5
│           └── gex_FindAllMarkers.xls          6
└── outs
    └── demo_summary.csv                        7

1. RNA library alignment BAM file.
2. Raw RNA expression matrix.
3. Cell-filtered RNA expression matrix.
4. Seurat object and downstream analysis results in RDS format.
5. Cell embedding coordinates, UMI counts, mitochondrial proportion, and related information.
6. Marker gene table generated from Seurat clustering results.
7. RNA/GEX quality-control statistics.