This page details the cellranger multi output structure for Singleplex Universal 3' and 5' Gene Expression (GEX), V(D)J, Antibody Capture (cell surface protein), and Barcode Enabled Antigen Mapping (Antigen Capture) data, using a 5' experiment as an example.

Upon completion, the cellranger multi pipeline will produce an outs/ directory with a structure similar to the following:

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├── config.csv
├── feature_reference.csv
├── filtered_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── filtered_feature_bc_matrix.h5
├── per_sample_outs
│   └── gex_fb_vdj_chr21
├── qc_library_metrics.csv
├── qc_report.html
├── qc_sample_metrics.csv
├── raw_cloupe.cloupe
├── raw_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── raw_feature_bc_matrix.h5
├── raw_molecule_info.h5
├── unassigned_alignments.bam
├── unassigned_alignments.bam.bai
├── vdj_b
│   ├── all_contig.bam
│   ├── all_contig.bam.bai
│   ├── all_contig.fasta
│   ├── all_contig.fasta.fai
│   ├── all_contig.fastq
│   ├── all_contig_annotations.bed
│   ├── all_contig_annotations.csv
│   └── all_contig_annotations.json
├── vdj_reference
│   ├── fasta
│   └── reference.json
└── vdj_t
    ├── all_contig.bam
    ├── all_contig.bam.bai
    ├── all_contig.fasta
    ├── all_contig.fasta.fai
    ├── all_contig.fastq
    ├── all_contig_annotations.bed
    ├── all_contig_annotations.csv
    └── all_contig_annotations.json

The files included at the top level may include:

• config.csv: a duplicate of the input config CSV file.
• feature_reference.csv: a duplicate of the input Feature Reference CSV file, if provided.
• filtered_feature_bc_matrix.h5: filtered feature-barcode matrix (containing only barcodes called as cells), concatenated across all samples, in HDF5 format.
• qc_library_metrics.csv: quality control report in CSV format for the entire experiment.
• qc_report.html: quality control report in HTML format for the entire experiment.
• qc_sample_metrics.csv: quality control report in CSV format by sample.
• raw_cloupe.cloupe: Loupe Browser file containing all samples and all cell-associated barcodes in the experiment.
• raw_feature_bc_matrix.h5: raw feature-barcode matrix (containing all barcodes) in HDF5 format.
• raw_molecule_info.h5: information about all molecules in the experiment. This file includes background and cell-associated barcodes from all samples in addition to valid barcodes that were not assigned to a sample.
• unassigned_alignments.bam: alignments from barcodes not assigned to any sample.
• unassigned_alignments.bam.bai: alignments from barcodes not assigned to any sample (index). In cases where the reference transcriptome is generated from a genome with very long chromosomes (>512 Mbp), Cell Ranger generates an unassigned_alignments.bam.csi index file instead.

Continue reading for descriptions of the directories contained within the top-level outputs.

In addition to the HDF5 format listed above, two directories contain the filtered (concatenated across all samples) and raw feature-barcode matrices in Market Exchange (MEX) Format:

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└── filtered_feature_bc_matrix
    ├── barcodes.tsv.gz
    ├── features.tsv.gz
    └── matrix.mtx.gz
...
└── raw_feature_bc_matrix
    ├── barcodes.tsv.gz
    ├── features.tsv.gz
    └── matrix.mtx.gz

Filtered outputs are provided in the per_sample_outs directory:

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└── gex_fb_vdj_chr21
    ├── aggregate_barcodes.csv
    ├── analysis
    ├── metrics_summary.csv
    ├── sample_alignments.bam
    ├── sample_alignments.bam.bai
    ├── sample_cloupe.cloupe
    ├── sample_filtered_barcodes.csv
    ├── sample_filtered_feature_bc_matrix
    ├── sample_filtered_feature_bc_matrix.h5
    ├── sample_molecule_info.h5
    ├── sample_raw_feature_bc_matrix
    ├── sample_raw_feature_bc_matrix.h5
    ├── vdj_b
    ├── vdj_t
    └── web_summary.html

• aggregate_barcodes.csv: shows antibody (and antigen) barcodes that were detected as aggregates with metrics. See this page for more information.
• analysis: secondary analysis results, including dimensionality reduction, clustering, and differential gene expression.
• metrics_summary.csv: experimental metrics in CSV format.
• sample_alignments.bam: Indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, as well as unaligned reads, annotated with barcode information.
• sample_alignments.bam.bai: Index file for the sample_alignments.bam. In cases where the reference transcriptome is generated from a genome with very long chromosomes (>512 Mbp), Cell Ranger generates a sample_alignments.bam.csi index file instead.
• sample_cloupe.cloupe: sample-specific Loupe Browser file
• sample_filtered_barcodes.csv: sample-specific filtered barcodes in CSV format.
• sample_filtered_feature_bc_matrix: sample-specific filtered feature-barcode matrix in Market Exchange (MEX) Format
• sample_filtered_feature_bc_matrix.h5: sample-specific filtered feature-barcode matrix (containing only barcodes called as cells within this sample) in HDF5 format.
• sample_molecule_info.h5: information about all molecules in the sample. This file includes background and cell-associated barcodes.
• sample_raw_feature_bc_matrix: sample-specific raw feature-barcode matrix in Market Exchange (MEX) Format
• sample_raw_feature_bc_matrix.h5: sample-specific raw feature-barcode matrix (containing all barcodes assigned to this sample) in HDF5 format.
• vdj_b: folder containing unfiltered 5' V(D)J analysis results for any B cells (cell-associated and background barcodes), described in the Raw Outputs section. This folder is only produced if a VDJ-B (BCR) library is included in the analysis.
• vdj_t: folder containing unfiltered V(D)J Immune Profiling analysis results for any T cell (cell-associated and background barcodes) expressing alpha-beta chains, described in the Raw Outputs section. This folder is only produced if a VDJ-T (TCR) library is included in the analysis.
• web_summary.html: sample-specific web summary HTML, a starting point for quality control.

For 5' Immune Profiling data, V(D)J outputs are provided in three or more directories:

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├── vdj_b
│   ├── all_contig.bam
│   ├── all_contig.bam.bai
│   ├── all_contig.fasta
│   ├── all_contig.fasta.fai
│   ├── all_contig.fastq
│   ├── all_contig_annotations.bed
│   ├── all_contig_annotations.csv
│   └── all_contig_annotations.json
├── vdj_reference
│   ├── fasta
│   └── reference.json
└── vdj_t
    ├── all_contig.bam
    ├── all_contig.bam.bai
    ├── all_contig.fasta
    ├── all_contig.fasta.fai
    ├── all_contig.fastq
    ├── all_contig_annotations.bed
    ├── all_contig_annotations.csv
    └── all_contig_annotations.json

• vdj_b: folder containing unfiltered 5' V(D)J analysis results for any B cells (cell-associated and background barcodes), described in the Raw Outputs section. This folder is only produced if a VDJ-B (BCR) library is included in the analysis.
• vdj_reference: a copy of the V(D)J reference used in the analysis.
• vdj_t: folder containing unfiltered V(D)J Immune Profiling analysis results for any T cell (cell-associated and background barcodes) expressing alpha-beta chains, described in the Raw Outputs section. This folder is only produced if a VDJ-T (TCR) library is included in the analysis.