10x Genomics
Spatial Gene Expression

Space Ranger, printed on 09/07/2024

Release notes for Space Ranger 1.2.2 (February 3, 2021):

Adds support for pyramid TIFFs, or TIFFs with multiple pages of the same image at different resolutions.
Fixes an issue where targeted samples run against new references would fail preflight.

Fixed an issue in aggr where files would fail to be copied on NFSv4 File Systems.
Disables multithreading in mkref to address an issue where mkref would fail on hardware without AVX support. This will be fixed in a future release.
Better error handling if the pipeline fails due to a missing .env.json file due to an incomplete copy of the application folder.

Targeted Gene Expression analysis is now available in Space Ranger 1.2 and is invoked by specifying the --target-panel option when running the spaceranger count command.
Space Ranger 1.2 introduces the new spaceranger targeted-compare pipeline for direct comparative analysis of matched parent Whole Transcriptome Amplification (WTA) and Targeted Gene Expression datasets.
Space Ranger includes the new spaceranger targeted-depth subcommand to estimate sequencing depths appropriate for Spatial Targeted Gene Expression experiments based on input WTA results and an associated target panel file.
A new command line option, --no-bam, instructs the pipeline not to construct BAM files.
The GTF file parsing methods have been changed and some GTF files with non-standard metadata fields may no longer be accepted by Space Ranger. You may need to reformat the metadata fields into a standard layout.
Performance improvements in reading FASTQ files, writing BAM files, and memory utilization in certain pipeline stages.
spaceranger aggr now outputs a t-SNE projection colored by the input sample.
Support for Gateway slides containing two standard 6mm capture areas per slide.

The --unknown-slide option for spaceranger testrun has been renamed --no-internet to reflect its intended use.
Fixed an issue in mkfastq that prevented the --filter-single-index option from working correctly.
Fixed an issue where files would fail to be copied on NFSv4 File Systems.
The --nuclei option was removed from spaceranger mkref.
The colors used in the web summary output to indicate fiducial alignment and tissue detection have been changed to avoid confusion with an H&E stained image.
The maximum number of colors (channels) in a fluorescence imaging sample has been increased to nine.
Fixed parsing of some non-standard FASTQ files to avoid errors.
Bug fixes for GTF files output by mkref:
- GTF attributes with duplicate keys (e.g., tag "value1"; tag "value2";) are handled correctly. Previously, only the last such attribute was kept.
- GTF attributes with unquoted integer values (e.g., exon_number 1;) are kept. Previously, they were removed.
- GTF lines end with semicolons.
- Unix line endings are used rather than DOS line endings, consistent with other Space Ranger outputs.
- Fixed problem parsing GTF files with semicolon delimiter inside quotes
Fixed a numerical stability issue in the PCA method that affected the analysis of some datasets.
BGI/MGI reads can now be analyzed using Space Ranger.

The duplicate flag (0x400) is set correctly in the secondary alignments (flag 0x100) of PCR duplicate reads and low-support UMI reads (xf:i:2)
Low-support UMI reads (xf:i:2) have the corrected barcode in UB:Z. Previously, it contained the raw barcode.
The duplicate flag (0x400) is set correctly in the secondary alignments (flag 0x100) of PCR duplicate reads and low-support UMI reads (xf:i:2)
Low-support UMI reads (xf:i:2) have the corrected barcode in UB:Z. Previously, it contained the raw barcode.
Reads that are excluded from analysis due to high-depth subsampling in targeted gene expression are unmapped and marked with (xf:i:32) in the BAM.

The minimum dimension for an input image to Space Ranger is 2000 pixels on a side. Even though the Loupe Manual Aligner may allow smaller images to be used during manual alignment, the pipeline will not process images that are smaller than the minimum. These limits will be made consistent in an upcoming release.
Loupe and Space Ranger currently do not support BigTIFF files that contain a multi-resolution image pyramid. We’re aware that some systems produce such files and we recommend converting such images externally to a single-resolution image at the highest resolution desired. We hope to address this issue in a future release.