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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 (currently available in the United States and Canada):

  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

We observe sensitivity gains in the analysis with the 2020-A reference compared to the previous cellranger/spaceranger reference. These are mainly due to an updated transcriptome annotation (Ensembl 93 → 98) and improved filtering of readthrough gene annotations. A number of genes (notably IGLC1) are uncounted or undercounted without this filtering step. Below are gains in sensitivity that we observed.

  • 1-3% relative increase in Median UMI Counts per spot
  • 1-2% relative increase in Median Genes per spot
  • 4-7% relative increase in Total Genes Detected
  • 1-3% increase in Reads Mapped Confidently to Transcriptome
  • 0.5% decrease in Reads Mapped Confidently to Intergenic Regions

Details about the specific steps used to correct these annotations can be found in the reference build scripts.

View steps to build references

  • Human reference (GRCh38) - 2020-A

    • Human reference (GRCh38) dataset required for Cell Ranger.
    Download Human Reference
    File size: 110.178 MB
    md5sum: dfd654de39bff23917471e7fcc7a00cd
    curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz"
  • Mouse reference (mm10) - 2020-A

    • Mouse reference (mm10) dataset required for Cell Ranger.
    Download Mouse Reference
    File size: 110.178 MB
    md5sum: 886eeddde8731ffb58552d0bb81f533d
    curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-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: 110.178 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: 110.178 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

The Single Cell Fixed RNA Profiling 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
Mouse Transcriptome

Other downloads

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