Cell Ranger7.1, printed on 11/23/2024
An overview of Cell Ranger outputs for different pipelines and products is described below, with links to detailed documentation for each section.
All pipelines produce all of their output in a single pipeline output directory, whose name depends on the pipeline:
--id argument is used, or if unspecified, the flow cell ID is used (e.g., HAWT7ADXX).--id argument is used.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.More information about the contents of the Cell Ranger pipeline output directory can be found in the Advanced section's Pipestance Structure page.
The Cell Ranger software strives to maintain compatibility with common analysis tools by using standard output file formats whenever possible. For example, the barcoded BAM files can be viewed in standard genome browsers such as IGV to verify alignment quality and other features. Data specific to 10x Genomics products, including cellular and molecular barcodes, can be accessed by third-party tools or scripts that can parse the additional elements utilized by Cell Ranger.
For primary analysis, the cellranger count and multi pipelines will output the following types of files:
Cell Ranger computes application results metrics for each supported library type. Supported library types are "Gene Expression" for standard gene expression data, and the Feature Barcode-specific library types "Antibody Capture", "CRISPR Guide Capture", "Cell Multiplexing", and "Custom" (user-defined assays that are neither Antibody nor CRISPR). Feature Barcode metrics will be computed and displayed only when one of these library types was used in the assay.
Metric descriptions for each supported library are available here:
The cellranger count pipeline for Gene Expression, Antibody Capture, CRISPR Guide Capture, and Targeted Gene Expression analysis will each output the types of files listed above. There are additional output files for Targeted Gene Expression and Feature Barcode libraries.
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' Targeted Gene Expression | 3' Targeted Gene Expression outputs |
| 3' Gene Expression + Antibody/CRISPR Guide Capture | See 3' Gene Expression outputs and either |
The cellranger multi pipeline for Gene Expression, Cell Multiplexing, and Fixed RNA Profiling analysis will each output similar types of files as in the count pipeline, although the outs/ hierarchy, layout, and some file names differ. For example, the web summary HTML layout differs from the count pipeline web summary. 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 + Cell Multiplexing (+ Antibody Capture/CRISPR Guide Capture) | Cell Multiplexing outputs |
| Fixed RNA Profiling Gene Expression (+ Antibody Capture) | Fixed RNA Profiling 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 reanalyze pipeline will produce a secondary analysis web summary and a .cloupe file within a secondary analysis output directory called outs/. See the secondary analysis page for details about reanalyzed outputs.