10x Genomics
Spatial Gene Expression

Space Ranger, printed on 11/13/2024

Release notes for Space Ranger 1.3.1 (November 1, 2021):

Adds an alert if image alignment would have produced a different result if the --reorient-images option was specified.
Update warning for low fraction of reads confidently mapped to the probe set to be more informative.
Unsets additional sysconfig environment variables prior to pipeline execution, which may otherwise interfere with the pipeline conda environment.
Fixes an issue with mkfastq when bcl2fastq requires LD_LIBRARY_PATH.

The recommended operating systems for Space Ranger 1.3.0 are CentOS 7 or Ubuntu 14 Linux variants or newer. CentOS 6 and Ubuntu 12 are still supported but have been deprecated. Support may be dropped in future versions.

Gene Expression analysis from formalin fixed paraffin embedded (FFPE) samples is now available in Space Ranger and is invoked by specifying the --probe-set option when running the spaceranger count command. Space Ranger 1.3.0 or later is required to analyze FFPE data.
A new --no-probe-filter option can be used to disable the default filtering of certain probes. See the documentation for more information.
A new probe aligner tailored for use with probe-based assays, such as Visium for FFPE, was developed. When the --probe-set option is invoked, Space Ranger aligns reads to the specified probe set to count oligo ligation events. See the algorithms for more details.
BAM output from probe-based assays includes a new tag pr:Z that indicates the probe to which a read aligns and specifies the gene ID, gene name, and a computational hash specific to the probe sequence.
Visium Spatial Gene Expression for FFPE ships with a new dual index set (Dual Index Kit TS Set A) distinct from the dual index set used for fresh frozen tissues (Dual Index Kit TT Set A). The dual index sets can be detected by spaceranger mkfastq based on their abbreviations (e.g., SI-TS-A1) in the samplesheet. Space Ranger 1.3.0 or later is necessary to detect Dual Index Kit TS Set A with spaceranger mkfastq.

Space Ranger now calculates the Moran's I spatial autocorrelation metric on a per-gene basis, highlighting genes with patterns of spatially coherent gene expression for presentation in Loupe Browser and in a new output file spatial_enrichment.csv.

The web summary output from Space Ranger now indicates whether the --reorient-images option was specified in order to enable automatic rotation of input images.
The web summary now differentiates probe-based, targeted, and whole genome analyses.
Space Ranger now uses Python 3 for Python-based stages.
The molecule_info.h5 and unfiltered feature-barcode matrix files (raw_feature_bc_matrix in H5 and MEX formats) will only contain barcodes with at least one read, rather than all barcodes in the whitelist.
A bug that prevented error messages from spaceranger mkref from displaying properly when processing GTF files was fixed.
A bug has been fixed in the graph-based clustering output: previously, in a sample with K clusters, the first K spot-associated barcodes (ordered as in the filtered feature-barcode matrix) may have been assigned incorrect cluster labels. This change does not affect the number of clusters output.
The --qc option has been deprecated from spaceranger mkfastq.