Space Ranger, printed on 07/01/2022
The Visium for FFPE assay uses 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.
Gene IDs and probe sequences are defined in the probe set reference CSV input file for spaceranger count. Three supporting files are provided: a BED file listing the reference genome coordinates for each probe, a CSV file listing probes with predicted off-target activity, which are excluded from analysis by default and a TSV file that contains gene name and description for each of the probes.