Cell Ranger pipelines generate all outputs within a single pipeline output directory, with the folder name matching the --id argument provided to the Cell Ranger pipelines.
Output files will appear in the outs/ subdirectory within this pipeline output directory. For example, a typical cellranger count analysis may display the following after completion:
cd /home/jdoe/runs
cellranger count --id=sample345 \
--transcriptome=/opt/refdata-gex-GRCh38-2020-A \
--fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
--indices=SI-3A-A1
Martian Runtime - v4.0.8
Running preflight checks (please wait)...
2016-01-01 10:23:52 [runtime] (ready) ID.sample345.CELLRANGER_CS.CELLRANGER.SETUP_CHUNKS
...
2012-01-01 12:10:09 [runtime] (join_complete) ID.sample345.CELLRANGER_CS.CELLRANGER.SUMMARIZE_REPORTS
Outputs:
- Run summary HTML: /home/jdoe/runs/sample345/outs/web_summary.html
- Run summary CSV: /home/jdoe/runs/sample345/outs/metrics_summary.csv
- BAM: /home/jdoe/runs/sample345/outs/possorted_genome_bam.bam
- BAM index: /home/jdoe/runs/sample345/outs/possorted_genome_bam.bam.bai
- Filtered feature-barcode matrices MEX: /home/jdoe/runs/sample345/outs/filtered_feature_bc_matrix
- Filtered feature-barcode matrices HDF5: /home/jdoe/runs/sample345/outs/filtered_feature_bc_matrix.h5
- Unfiltered feature-barcode matrices MEX: /home/jdoe/runs/sample345/outs/raw_feature_bc_matrix
- Unfiltered feature-barcode matrices HDF5: /home/jdoe/runs/sample345/outs/raw_feature_bc_matrix_h5.h5
- Secondary analysis output CSV: /home/jdoe/runs/sample345/outs/analysis
- Per-molecule read information: /home/jdoe/runs/sample345/outs/molecule_info.h5
- Loupe Browser file: /home/jdoe/runs/sample345/outs/cloupe.cloupe
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, and/home/jdoe/runs/sample345/outs/contains the final pipeline output files.
For primary analysis, the cellranger count, cellranger vdj, and cellranger multi pipelines will output the following types of files:
- Web summary HTML (
count,multi,vdj) - Metrics summary CSV
- BAM
- Raw and filtered feature-barcode matrices (MEX, H5)
- Secondary analysis files (CSV)
- Molecule info (H5)
- Loupe files (.cloupe and .vloupe)
The sections below provide overviews for different Cell Ranger pipelines and supported Chromium data types.
| Library type | Outputs documentation |
|---|---|
| 3'/5' Multiplex Gene Expression with or without Feature Barcode, including On-chip Multiplexing (OCM), Hashing with Antibody Capture, and 3' CellPlex | 3'/5' Sample multiplexing outputs |
| 3'/5' Singleplex Gene Expression with or without Feature Barcode | 3'/5' Singleplex outputs |
| Flex Singleplex & Multiplex Gene Expression (+ Antibody Capture/CRISPR Guide Capture) | Flex v1/v2 outputs |
The cellranger count pipeline for Gene Expression, Antibody Capture, and CRISPR Guide Capture, will each output the types of files listed above.
For specific analysis output descriptions, select the library type below to go to the associated outputs documentation pages:
| Library type | Outputs documentation |
|---|---|
| 3' Gene Expression | 3' Gene Expression outputs |
| 3' Gene Expression + Antibody/CRISPR Guide Capture | See 3' Gene Expression outputs and either Antibody output files and metrics or CRISPR output files and metrics |
| Library type | Outputs documentation |
|---|---|
| 5' V(D)J for T and B cells | V(D)J outputs |
The cellranger aggr pipeline will output a web summary, a filtered matrix, and a .cloupe file all within a directory called outs/. See aggr outputs section for more information.
The cellranger annotate pipeline will output a new web summary with annotations and other files that help map barcodes to annotated cell types. These outputs are listed and described in on the cell annotations page.