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.
Download Human ReferenceFile size: 110.178 MBmd5sum: 26151804338ae4d4b44151232bd64b50
- Human reference (GRCh38) dataset required for Space Ranger.
mm10 Reference - 2020-A (June 23, 2020)
Download Mouse ReferenceFile size: 110.178 MBmd5sum: 24ee09ad620a9eb2753763fa068edf1f
- Mouse reference (mm10) dataset required for Space Ranger.
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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
View more details about probe sets
Human Transcriptome v2
Human Transcriptome v1
Mouse Transcriptome v1
View the minimum requirements to run Space Ranger pipelines
View instructions on how to install Space Ranger