Cell Ranger4.0, printed on 04/19/2024
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 by third-party tools or scripts that can parse the additional elements utilized by Cell Ranger.
The cellranger count pipeline for gene expression, antibody, CRISPR, and targeted analysis will all output the following files:
In addition to the files listed above, the CRISPR pipeline will also output a CRISPR output CSV file.
The antibody pipeline will produce all of the files listed above and an Antibody t-SNE CSV file.
The cellranger reanalyze pipeline will produce a secondary analysis web summary, a .cloupe file within a secondary analysis output directory called outs.
The cellranger aggr pipeline will output a web summary, matrices and a .cloupe file all within a directory called outs.
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 may look like:
$ 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 - v4.0.0 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.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.