Spatial Gene Expression
Space Ranger, printed on 12/10/2023
Release Notes for Space Ranger 1.1.0
- Support for fluorescence imaging input such as IHC/IF.
- Aggregation of multiple datasets.
- Optional automatic rotation of slide images.
- Space Ranger 1.1 runs two to five times faster than Space Ranger 1.0, depending on the sequencing data, and reduces disk I/O by half.
- The fraction of reads mapped confidently to a gene was improved by up to 9% by trimming template switch oligo (TSO) sequence from the 5' end of read 2 and poly-A from the 3' end prior to alignment.
- Space Ranger now provides consistent sensitivity across a wider range of read lengths, from 70 bp reads to 120 bp reads, enabling use of smaller sequencing kits.
- The recommended references for mouse and human have been updated (new version: 2020-A). The new references remove annotations with weak evidence that prevent alignment to legitimate annotations.
- Space Ranger 1.1 uses Orbit to perform transcriptome alignment, which leverages a modified STAR v2.7.2a. These modifications provide compatibility with “versionGenome 20201” references, such as those generated by STAR v2.5.1b. In Space Ranger 1.1 we still provide and use STAR v2.5.1b for other purposes such as spaceranger mkref. In our testing we did not note any differences in transcriptome alignments between the STAR shipped in Space Ranger 1.0 (STAR v2.5.1b), STAR v2.7.2a, or Orbit.