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, a typical cellranger-arc count may look like:
$ cd /home/jdoe/runs
$ cellranger-arc count --id=sample345 \
--reference=/opt/refdata-cellranger-arc-GRCh38 \
--libraries=/home/jdoe/libraries.csv \
Martian Runtime - v4.0.5
Running preflight checks (please wait)...
2021-04-28 09:46:04 [runtime] (ready) ID.sample345.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF
...
2021-04-28 10:13:24 [runtime] (join_complete) ID.sample345.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS
Outputs:
- Secondary analysis outputs:
clustering:
atac: {
graphclust:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/graphclust/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/graphclust/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/graphclust/differential_accessibility.csv
kmeans_2_clusters:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_2_clusters/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_2_clusters/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_2_clusters/differential_accessibility.csv
kmeans_3_clusters:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_3_clusters/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_3_clusters/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_3_clusters/differential_accessibility.csv
kmeans_4_clusters:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_4_clusters/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_4_clusters/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_4_clusters/differential_accessibility.csv
kmeans_5_clusters:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_5_clusters/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_5_clusters/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/atac/kmeans_5_clusters/differential_accessibility.csv
}
gex: {
graphclust:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/graphclust/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/graphclust/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/graphclust/differential_accessibility.csv
kmeans_2_clusters:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_2_clusters/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_2_clusters/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_2_clusters/differential_accessibility.csv
kmeans_3_clusters:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_3_clusters/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_3_clusters/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_3_clusters/differential_accessibility.csv
kmeans_4_clusters:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_4_clusters/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_4_clusters/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_4_clusters/differential_accessibility.csv
kmeans_5_clusters:
clusters: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_5_clusters/clusters.csv
differential_expression: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_5_clusters/differential_expression.csv
differential_accessibility: /home/jdoe/runs/sample345/outs/analysis/clustering/gex/kmeans_5_clusters/differential_accessibility.csv
}
dimensionality_reduction:
atac: {
lsa_components: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/atac/lsa_components.csv
lsa_dispersion: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/atac/lsa_dispersion.csv
lsa_features_selected: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/atac/lsa_features_selected.csv
lsa_projection: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/atac/lsa_projection.csv
lsa_variance: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/atac/lsa_variance.csv
tsne_projection: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/atac/tsne_projection.csv
umap_projection: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/atac/umap_projection.csv
}
gex: {
pca_components: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/gex/pca_components.csv
pca_dispersion: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/gex/pca_dispersion.csv
pca_features_selected: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/gex/pca_features_selected.csv
pca_projection: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/gex/pca_projection.csv
pca_variance: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/gex/pca_variance.csv
tsne_projection: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/gex/tsne_projection.csv
umap_projection: /home/jdoe/runs/sample345/outs/analysis/dimensionality_reduction/gex/umap_projection.csv
}
feature_linkage:
feature_linkage_matrix: /home/jdoe/runs/sample345/outs/analysis/feature_linkage/feature_linkage_matrix.h5
feature_linkage: /home/jdoe/runs/sample345/outs/analysis/feature_linkage/feature_linkage.bedpe
tf_analysis:
filtered_tf_bc_matrix: /home/jdoe/runs/sample345/outs/analysis/tf_analysis/filtered_tf_bc_matrix
filtered_tf_bc_matrix_h5: /home/jdoe/runs/sample345/outs/analysis/tf_analysis/filtered_tf_bc_matrix.h5
peak_motif_mapping: /home/jdoe/runs/sample345/outs/analysis/tf_analysis/peak_motif_mapping.bed
- Run summary HTML: /home/jdoe/runs/sample345/outs/web_summary.html
- Run summary metrics CSV: /home/jdoe/runs/sample345/outs/summary.csv
- Per barcode summary metrics: /home/jdoe/runs/sample345/outs/per_barcode_metrics.csv
- Filtered feature barcode matrix MEX: /home/jdoe/runs/sample345/outs/filtered_feature_bc_matrix
- Filtered feature barcode matrix HDF5: /home/jdoe/runs/sample345/outs/filtered_feature_bc_matrix.h5
- Raw feature barcode matrix MEX: /home/jdoe/runs/sample345/outs/raw_feature_bc_matrix
- Raw feature barcode matrix HDF5: /home/jdoe/runs/sample345/outs/raw_feature_bc_matrix.h5
- Loupe browser visualization file: /home/jdoe/runs/sample345/outs/cloupe.cloupe
- GEX Position-sorted alignments BAM: /home/jdoe/runs/sample345/outs/gex_possorted_bam.bam
- GEX Position-sorted alignments BAM index: /home/jdoe/runs/sample345/outs/gex_possorted_bam.bam.bai
- GEX Per molecule information file: /home/jdoe/runs/sample345/outs/gex_molecule_info.h5
- ATAC Position-sorted alignments BAM: /home/jdoe/runs/sample345/outs/atac_possorted_bam.bam
- ATAC Position-sorted alignments BAM index: /home/jdoe/runs/sample345/outs/atac_possorted_bam.bam.bai
- ATAC Per fragment information file: /home/jdoe/runs/sample345/outs/atac_fragments.tsv.gz
- ATAC Per fragment information index: /home/jdoe/runs/sample345/outs/atac_fragments.tsv.gz.tbi
- ATAC peak locations: /home/jdoe/runs/sample345/outs/atac_peaks.bed
- ATAC smoothed transposition site track: /home/jdoe/runs/sample345/outs/atac_cut_sites.bigwig
- ATAC peak annotations based on proximal genes: /home/jdoe/runs/sample345/outs/atac_peak_annotation.tsv
Pipestance completed successfully!
In this case,
/home/jdoe/runs/is where the pipeline was run,/home/jdoe/runs/sample345/is the top-level output directory containing pipeline metadata/home/jdoe/runs/sample345/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/2.0/analysis/transposition-counts)
-
Gene Expression outputs:
More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.