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10x Genomics
Chromium Single Cell Multiome ATAC + Gene Exp.

Understanding Output

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 - v4.0.1
 
Running preflight checks (please wait)...
2020-09-01 09:46:04 [runtime] (ready)           ID.sample345.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF
...
2020-09-01 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,

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.