Cell Ranger ARC strives to maintain compatibility with common analysis tools by using standard output file formats whenever possible. The Chromium-specific data, including cellular and molecular barcodes, can be accessed by third-party tools or scripts that can parse the additional elements utilized by Cell Ranger ARC.

All pipeline outputs are produced in a single pipeline output directory, which is specified by the --id argument for both cellranger-arc count and cellranger-arc mkfastq (defaults to the flow cell serial number, e.g., HAWT7ADXX when the --id argument is not specified).

Output files will appear in the outs/ subdirectory within this pipeline output directory. For example:

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├── analysis
│   ├── clustering
│   │   ├── atac
│   │   │   ├── peaks_graphclust
│   │   │   │   ├── clusters.csv
│   │   │   │   ├── differential_accessibility.csv
│   │   │   │   └── differential_expression.csv
│   │   │   ├── peaks_kmeans_2_clusters
│   │   │   │   ├── clusters.csv
│   │   │   │   ├── differential_accessibility.csv
│   │   │   │   └── differential_expression.csv
│   │   │   ├── peaks_kmeans_3_clusters
│   │   │   │   ├── clusters.csv
│   │   │   │   ├── differential_accessibility.csv
│   │   │   │   └── differential_expression.csv
│   │   │   ├── peaks_kmeans_4_clusters
│   │   │   │   ├── clusters.csv
│   │   │   │   ├── differential_accessibility.csv
│   │   │   │   └── differential_expression.csv
│   │   │   └── peaks_kmeans_5_clusters
│   │   │       ├── clusters.csv
│   │   │       ├── differential_accessibility.csv
│   │   │       └── differential_expression.csv
│   │   └── gex
│   │       ├── gene_expression_graphclust
│   │       │   ├── clusters.csv
│   │       │   ├── differential_accessibility.csv
│   │       │   └── differential_expression.csv
│   │       ├── gene_expression_kmeans_2_clusters
│   │       │   ├── clusters.csv
│   │       │   ├── differential_accessibility.csv
│   │       │   └── differential_expression.csv
│   │       ├── gene_expression_kmeans_3_clusters
│   │       │   ├── clusters.csv
│   │       │   ├── differential_accessibility.csv
│   │       │   └── differential_expression.csv
│   │       ├── gene_expression_kmeans_4_clusters
│   │       │   ├── clusters.csv
│   │       │   ├── differential_accessibility.csv
│   │       │   └── differential_expression.csv
│   │       └── gene_expression_kmeans_5_clusters
│   │           ├── clusters.csv
│   │           ├── differential_accessibility.csv
│   │           └── differential_expression.csv
│   ├── dimensionality_reduction
│   │   ├── atac
│   │   │   ├── lsa_components.csv
│   │   │   ├── lsa_dispersion.csv
│   │   │   ├── lsa_features_selected.csv
│   │   │   ├── lsa_projection.csv
│   │   │   ├── lsa_variance.csv
│   │   │   ├── tsne_projection.csv
│   │   │   └── umap_projection.csv
│   │   └── gex
│   │       ├── pca_components.csv
│   │       ├── pca_dispersion.csv
│   │       ├── pca_features_selected.csv
│   │       ├── pca_projection.csv
│   │       ├── pca_variance.csv
│   │       ├── tsne_projection.csv
│   │       └── umap_projection.csv
│   ├── feature_linkage
│   │   ├── feature_linkage.bedpe
│   │   └── feature_linkage_matrix.h5
│   └── tf_analysis
│       ├── filtered_tf_bc_matrix
│       │   ├── barcodes.tsv.gz
│       │   ├── matrix.mtx.gz
│       │   └── motifs.tsv
│       ├── filtered_tf_bc_matrix.h5
│       └── peak_motif_mapping.bed
├── atac_cut_sites.bigwig
├── atac_fragments.tsv.gz
├── atac_fragments.tsv.gz.tbi
├── atac_peak_annotation.tsv
├── atac_peaks.bed
├── cloupe.cloupe
├── filtered_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── filtered_feature_bc_matrix.h5
├── gex_molecule_info.h5
├── per_barcode_metrics.csv
├── raw_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── raw_feature_bc_matrix.h5
├── summary.csv
└── web_summary.html

In this case,

• /home/jdoe/runs/ is where the pipeline was run,
• / is the top-level output directory containing pipeline metadata
• /outs/ contains the final pipeline output files.

The contents of this outs/ directory contain the data that is described in the remainder of this section:

• Multiomic outputs:

  • Web summary HTML, run summary metrics, and per barcode summary metrics
  • Secondary analysis including feature linkage
  • Feature-barcode matrices in MEX and HDF5 formats

• ATAC outputs:

  • ATAC position-sorted alignments BAM
  • ATAC peaks and ATAC peak annotations
  • ATAC per fragment information file and ATAC smoothed transposition site track](/support/software/cell-ranger-arc/2.1/analysis/transposition-counts)

• Gene Expression outputs:

  • GEX position-sorted alignments BAM
  • GEX molecule info HDF5

More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.