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To set up and run Cell Ranger on Linux, please follow the steps below, or skip download and installation and get started with 10x Cloud Analysis.

  1. Check system requirements
  2. Download Cell Ranger
  3. Download References (Optional)
  4. Download Probe Sets (Optional)
  5. Install Cell Ranger
  6. 10x Genomics Cloud Analysis (Optional)

References

New versions of the human and mouse reference transcriptomes based on the Ensembl v110 annotations are now available for download. Details are available in the reference release notes.

Steps to build references Reference release notes Prebuilt V(D)J reference details Download 2020-A references

  • Human reference (GRCh38) - 2024-A

    • Human reference (GRCh38) dataset required for Cell Ranger.
    Download Human Reference
    File size: 11 GB
    md5sum: a7b5b7ceefe10e435719edc1a8b8b2fa
    curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz"

  • Mouse reference (GRCm39) - 2024-A

    • Mouse reference (GRCm39) dataset required for Cell Ranger.
    Download Mouse Reference
    File size: 9.7 GB
    md5sum: 37c51137ccaeabd4d151f80dc86ce0b3
    curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCm39-2024-A.tar.gz"

  • Rat reference (mRatBN7.2) - 2024-A

    • Rat reference (mRatBN7.2) dataset required for Cell Ranger.
    Download Rat Reference
    File size: 9.5 GB
    md5sum: 34d4af0874a45dfa03436efe4eaec2fe
    curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mRatBN7-2-2024-A.tar.gz"

  • Human (GRCh38) and mouse (GRCm39) reference - 2024-A

    • Human (GRCh38) and mouse (GRCm39) reference dataset for Cell Ranger.
    Download Reference
    File size: 11 GB
    md5sum: b2d628e6c6813e1396989a9a9ca2ef23
    curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38_and_GRCm39-2024-A.tar.gz"

Download is unavailable on mobile devices.

  • Human V(D)J reference (GRCh38)

    • Human reference (GRCh38/Ensembl/10x) dataset required for Cell Ranger V(D)J.
    Download Human Reference
    File size: 3.3 MB
    md5sum: 65b5b033723b07fc1bb5375e5645761c
    curl -O "https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0.tar.gz"

  • Mouse V(D)J reference (GRCm38)

    • Mouse reference (GRCm38/Ensembl/10x) dataset required for Cell Ranger V(D)J.
    Download Mouse Reference
    File size: 3.5 MB
    md5sum: c6f41db8f67aa83b04d64ba1ae96e681
    curl -O "https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0.tar.gz"

Download is unavailable on mobile devices.

Probe Sets v1.1

The Flex assays use probes targeting protein coding genes in the human or mouse transcriptomes. Each probe consists of a pair of oligonucleotides hybridized to the targeted transcript and are subsequently ligated.

View more details about probe sets
Probe Barcode Sequence
Human Transcriptome
  • Probe Set CSV

    Input for cellranger multi pipeline

  • Probe Set Metadata TSV
  • Probe Set BED
  • Possible Off-Target Probes CSV
Mouse Transcriptome

Other downloads

Telemetry

Compute platforms

Compute platforms

View options for compute platforms

System requirements

System requirements

View the minimum requirements to run Cell Ranger pipelines

Installation

Cell Ranger installation

View instructions on how to install Cell Ranger