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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):
- Check system requirements
- Download Cell Ranger
- Download References (Optional)
- Download Probe Sets (Optional)
- Install Cell Ranger
- 10x Genomics Cloud Analysis (Optional)
Cell Ranger 7.2.0 (Sep 13, 2023)
- Chromium Single Cell Software Suite
- Self-contained, relocatable tar file. Does not require centralized installation.
- Contains binaries pre-compiled for CentOS/RedHat 7.0 and Ubuntu 14.04.
- Runs on Linux systems that meets the minimum compute requirements.
tar.gz compression
Download for Linux 64-bit (tar.gz)File size: 653 MBmd5sum: 85e2573e80a6f8656a42ff09460463e6- curl
- wget
curl -o cellranger-7.2.0.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-7.2.0.tar.gz?Expires=1695729999&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=UiAU-XhRIc6lg7hpNqK4Y09EMx2v-PvhoXlJdsRpEvTbXaxEocHQNpte4rV9t3O7HdU-t1v2Ub~~mh~-uvgShU0rMiTn7d5Z4UjClNfIbFvbJdkqHIIUFAlo6jUkYSfn-BQtK3dyynTXdcLJujYKYArMwW-7JcJYyh4iqE6HkDZR0Edlx61HZzTe~UZI3c5VZQMKaOMwTT~ZzqukFSU63dCYgtOZvmYpiknoGsanU~N7SIQ7OGNI7CCIklw7rrcGz628bt9D885f6YfLN05oHL4QokrPrWFX7-nH3St17k75fw-mIyOO-2YGZQoVfggt7G6HJFWacKiGKHF8M9vs8w__"tar.xz compression
Download for Linux 64-bit (tar.xz)File size: 436 MBmd5sum: 64f2c8c813dbdc030a80ad59096dc9a2- curl
- wget
curl -o cellranger-7.2.0.tar.xz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-7.2.0.tar.xz?Expires=1695729999&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=QydlUutRIDTeOdF-xb2Pp8qoKYPtO~i0E0sC5GL5IZfZfuRzUrKQfsH2GRQj0LWoSQk0MnLyaj~8qx3RqvmDmQ5NlK6~n~XMS~3duoa6CAF0-RK3Rs4Uv1SRSqMlrA2oATg4RumQ-DIk39zmeqoWb3v3aT7AZz8JXRn4ghUhriBta1zquWlCJlHZwAmicXjvdN3is9poEMU22wQ5Y8xdKdtm~knNicprNItlL2tFXieXWtzjRgLbG7LuYXOnBXhCyPnpj4ALpcCLaMQqTc645fbTe0U0ptLnc1RHQ96T0fErSDq~1Q9j-i-2f0Gqvo8ZmP5VC8WQhSxrLXDDGvLqcQ__"
Download is unavailable on mobile devices.
Cell Ranger 7.2.0 highlights
- New feature: Supports the analysis of Multiplexed Gene Expression with Antibody Capture (Cell Surface Protein)
- New feature: Supports the aggregation of BEAM (Antigen Capture) libraries with cellranger aggr
- Several improvements to the web summary output files generated by cellranger multi and aggr pipelines
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 ReferenceFile size: 110.178 MBmd5sum: dfd654de39bff23917471e7fcc7a00cd- curl
- wget
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 ReferenceFile size: 110.178 MBmd5sum: 886eeddde8731ffb58552d0bb81f533d- curl
- wget
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 ReferenceFile size: 110.178 MBmd5sum: 65b5b033723b07fc1bb5375e5645761c- curl
- wget
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 ReferenceFile size: 110.178 MBmd5sum: c6f41db8f67aa83b04d64ba1ae96e681- curl
- wget
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
- Probe Set CSV v1.0
Input for cellranger multi pipeline
- Probe Set Metadata TSV v1.0
- Probe Set CSV v1.0.1
Input for cellranger multi pipeline
- Probe Set Metadata TSV v1.0.1
- Probe Set BED
- Possible Off-Target Probes CSV
Mouse Transcriptome
- Probe Set CSV v1.0
Input for cellranger multi pipeline
- Probe Set CSV v1.0.1
Input for cellranger multi pipeline
- Probe Set BED
- Possible Off-Target Probes CSV
- Probe Set Metadata TSV
Other downloads
Sample Index Set Sequences
- Chromium Single Cell 3' v2 CSV
- Chromium Single Cell 3' v2 JSON
- Chromium Single Cell 3' v1 CSV
- Chromium Single Cell 3' v1 JSON
- Gemcode Single Cell 3' CSV
- Gemcode Single Cell 3' JSON
- Chromium Single Cell 5' CSV
- Chromium Single Cell 5' JSON
- Chromium Single Cell 5' with Feature Barcodes CSV
- Chromium Single Cell 5' with Feature Barcodes JSON
Compute Platforms
View options for compute platforms
System requirements
View the minimum requirements to run Cell Ranger pipelines
Installation
View instructions on how to install Cell Ranger