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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.
- Check system requirements
- Download Cell Ranger
- Download References (Optional)
- Download Probe Sets (Optional)
- Install Cell Ranger
- 10x Genomics Cloud Analysis (Optional)
Cell Ranger 8.0.1 (May 15, 2024)
- 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: 702 MBmd5sum: 1d08d8005b026fc1ca3c867bc67b2dbdcurlwgetcurl -o cellranger-8.0.1.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-8.0.1.tar.gz?Expires=1732244166&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=mQ2N8ARz7J81M01jQav1bKZ~cz~c5oKJ-5qPH4SKlaDODLLAkQL99v193NEN-9M~uW~TNaAN6jOwyzgIZIFpEBbNJTG655WV1bS~T92jJfnK1KaBBH8sFkiac-JtOrKvfRXWQmEweLdSIvOF1u-f7M4e4t9xWg9GnW8gaIeCpNolNsJd7uFFqJThrfo7w679VQsC6J-jTTlQtjYyZS1yL~FqpJvP08uvaMSuPDByxMF8HnSrMDA-DQIOhK5Pt3H4E2BXGv4FgxAU7rnVSU8yX8LGa-atb76LlAxrp94sg2cP-R1PFVzsONxIptpoNGe9fp3SjStn0x5GP6lRrv8RNw__"tar.xz compression
Download for Linux 64-bit (tar.xz)File size: 453 MBmd5sum: 5d112b68f8819d50e54a9f3809cf5533curlwgetcurl -o cellranger-8.0.1.tar.xz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-8.0.1.tar.xz?Expires=1732244166&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=gzSJJ8BZAfMpWbJiG~6MY8AYnSIsN1Ru6-jNz7sKjlylsbivYyAjIi-yQvHY15mkqpsQeu33eFFmDz8ZYJSBo1GBq13l56xBuHZuRrCyWt~IiyXY6Wjn1TarYI2EMzlnOFZxU7WPgtvD7wkdi9ziZFVaMU-Lc5SHRwHL8B~rEugZNKrqJ~TY88IhzacBnbpuNbRw8PfLwteLIp~VG2XESghtF2WZXIBkal7C0M9FMd354~Pzlh6XqRoI~s5QNO478oZMgeDN94lA4RMPkuAI-N3VO-so5ehS-il0k6rtQP8N1SjEH1zfihl8ddAhUePkrCe~yP26nrHEKuZr7GaVfA__"
Download is unavailable on mobile devices.
Cell Ranger 8.0.1 highlights
- New feature: Supports the analysis of Chromium GEM-X Single Cell Gene Expression v4 and Chromium GEM-X Single Cell Immune Profiling v3 libraries
- Support for Low Throughput (LT) libraries has been disabled
- v8.0.1 fixes bugs and introduces a new optional parameter (min-crispr-umi) to customize the minimum number of CRISPR guide RNA UMIs for protospacer detection
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.
Human reference (GRCh38) - 2024-A
- Human reference (GRCh38) dataset required for Cell Ranger.
Download Human ReferenceFile size: 11 GBmd5sum: a7b5b7ceefe10e435719edc1a8b8b2facurlwgetcurl -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 ReferenceFile size: 9.7 GBmd5sum: 37c51137ccaeabd4d151f80dc86ce0b3curlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCm39-2024-A.tar.gz"Human (GRCh38) and mouse (GRCm39) reference - 2024-A
- Human (GRCh38) and mouse (GRCm39) reference dataset for Cell Ranger.
Download ReferenceFile size: 11 GBmd5sum: b2d628e6c6813e1396989a9a9ca2ef23curlwgetcurl -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 ReferenceFile size: 3.3 MBmd5sum: 65b5b033723b07fc1bb5375e5645761ccurlwgetcurl -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: 3.5 MBmd5sum: c6f41db8f67aa83b04d64ba1ae96e681curlwgetcurl -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 setsProbe 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