Cell Ranger ARC2.0, printed on 11/23/2024
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:
More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.