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:
├── 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/latest/analysis/transposition-counts)
-
Gene Expression outputs:
More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.