10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger3.1, printed on 12/03/2024

Understanding Output

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. The Chromium-specific data, including cellular and molecular barcodes, can be accessed via any third-party tools or scripts that can parse the additional elements utilized by Cell Ranger.

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

• For cellranger mkfastq, the flowcell serial number is used (e.g., HAWT7ADXX)
• For cellranger count, aggr and reanalyze, the --id argument is used

Output files will appear in the outs/ subdirectory within this pipeline output directory. For example, a typical cellranger count may look like:

$ cd /home/jdoe/runs
$ cellranger count --id=sample345 \
                 --transcriptome=/opt/refdata-cellranger-GRCh38-3.0.0 \
                 --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
                 --indices=SI-3A-A1 \
                 --expect-cells=1000
 
Martian Runtime - v3.2.3
 
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 Cell 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.

The contents of this outs/ directory contain the data that is described in the remainder of this section: run summary HTML, run analysis, feature-barcode matrices MEX and HDF5, barcoded BAMs, and molecule info HDF5.

More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.