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Cell Ranger


Loupe

10x Genomics
Chromium Single Cell Gene Expression

Understanding Outputs

An overview of Cell Ranger outputs for different pipelines and products is described below, with links to detailed documentation for each section.

Table of Contents

Overview of output structure

All pipelines produce all of their output in a single pipeline output directory, whose name depends on the pipeline:

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 \
                 --expect-cells=1000
 
Martian Runtime - v4.0.6
 
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,

More information about the contents of the Cell Ranger pipeline output directory can be found in the Advanced section's Pipestance Structure page.

Cell Ranger output file overview

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.

Metrics descriptions for each supported library are available here:

Primary analysis

cellranger count

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 and go to the associated outputs documentation pages:

Library type Outputs documentation
3' Gene Expression 3' Gene Expression outputs
3' Targeted Gene Expression See Output files section of Targeted Gene Expression analysis
  • Secondary analysis: Targeted-Compare 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
  • cellranger multi

    The cellranger multi pipeline for Gene Expression and Cell Multiplexing analysis will output similar types of files as in the count pipeline, although the outs/ hierarchy and some file names differ. These files are described in more detail on the Cell Multiplexing outputs and metrics pages.

    Secondary analysis

    cellranger aggr

    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.

    cellranger reanalyze

    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.