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To set up and run Space Ranger, please follow the following steps:
Space Ranger 2.1.0 (May 16, 2023)
- Visium Spatial 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: 707 MBmd5sum: ee94c453c44770b2b69d6be46b948e3e- curl
- wget
curl -o spaceranger-2.1.0.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.1.0.tar.gz?Expires=1695953592&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=NyTq-5p77u0CaSaI1OrQj75mJi7kJhEBNsO~wWsrgzv~3Pt4iG4rHRYaBcTbQK2eh47kTzIwAkCjtmSWGnGRS4GYuDbEzBK8oC-cLWaLpOrkU6OjRiRqc1a~l6ix26vWkyvphw2ZLSchS9mZGrrJ14~dLdv5dpUh1kOqVSbIoQrDFmTB5lzY5oR3qVT9gc5mFBgg5eTrTtamAynsIOfhfBHT7FmXFz74bg~Nh6hN0aH1eZy0ohiw37RPl1-pxNjxyMRBZZvD2B1bCSu0ehSlireso4JOjl6JmlA-onvE6Wiw6r9n3CaJeR3T~SpZ~a~io~zNs7oTbF9U8dCUEYa4EA__"
tar.xz compression
Download for Linux 64-bit (tar.xz)File size: 465 MBmd5sum: a0d90129a81c41cbdd728e23a4d25161- curl
- wget
curl -o spaceranger-2.1.0.tar.xz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.1.0.tar.xz?Expires=1695953592&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=YTrfYBDcgA8CAHvPe8YLKMHWB~w~fbbpkNbe6GdkHW0PEyRYLP4wVVz6jPy4Phn14RZvLjxh-G8wwasxWQK-EiW6gWZUERjdehO7QQRdjV~EaS4lCLLhqt5chZALA5wOmTLp4AH07Z1q3A1WCyLcnkh~cPlbB0uR4SN6fF6z7-GAj6Fk7NpETqVFPBsfqVwR802ugF8Onr4cmbrxL2xJG9WYl-cPTL9~siPrmot0J6QUpFAlMw2Zyf48zs-eNemfNvp92jHoKA7Gx5sai41uO2eCJJS19Mv2wv9iUuLktEWLQZUkzvfCOwm8EB6~-vjibgI89c0BDxIdgDZsQ33tYw__"
Download is unavailable on mobile devices.
Space Ranger 2.1.0 highlights
- New feature: Gene + Protein Expression on Visium CytAssist.
- New feature: Reference-free spot deconvolution.
- Added support for bigtiff (btf, tf2, and tf8) image file extensions.
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.
Human reference (GRCh38) dataset required for Space Ranger.
- Human reference (GRCh38) dataset required for Space Ranger.
Download Human ReferenceFile size: 110.178 MBmd5sum: 26151804338ae4d4b44151232bd64b50- curl
- wget
curl -O "https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gz"
mm10 Reference - 2020-A (June 23, 2020)
- Mouse reference (mm10) dataset required for Space Ranger.
Download Mouse ReferenceFile size: 110.178 MBmd5sum: 24ee09ad620a9eb2753763fa068edf1f- curl
- wget
curl -O "https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-mm10-2020-A.tar.gz"
Download is unavailable on mobile devices.
Probe Sets
The Visium for FFPE and the Visium CytAssist Spatial Gene and Protein Expression for FFPE 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
Human Transcriptome v2
- Probe Set CSV v2
Input for spaceranger count pipeline, CytAssist compatible
- Probe Set BED v2
- Possible Off-Target Probes CSV v2
- Probe Set Metadata TSV v2
- Probe Set Metadata Excel Spreadsheet v2
Human Transcriptome v1
- Probe Set CSV v1
Input for spaceranger count pipeline
- Probe Set BED v1
- Possible Off-Target Probes CSV v1
- Probe Set Metadata TSV v1
- Probe Set Metadata Excel Spreadsheet v1
Mouse Transcriptome v1
- Probe Set CSV v1
Input for spaceranger count pipeline, CytAssist compatible
- Probe Set BED v1
- Possible Off-Target Probes CSV v1
- Probe Set Metadata TSV v1
- Probe Set Metadata Excel Spreadsheet v1
Other downloads
System requirements
View the minimum requirements to run Space Ranger pipelines
Installation
View instructions on how to install Space Ranger