Question: What genes will not be detected by the Transcriptome Probe Panels?
Answer: In an effort to balance sensitivity, specificity and limit wasted data our design started with the high confidence genes annotated in APPRIS, so the starting point was closer to 19,500 genes than 22000. The list was limited further by excluding mitochondrial and ribosomal genes, as well as rearranged immune-related genes and read-through genes.
For the remaining genes, probes were designed against the GENCODE basic transcripts. Probes predicted to have some off-target activity to homologous genes or sequences are excluded from analysis by default. This is where the ~18000 number comes from. Customers can include UMI counts from all probes, including those with potential off-target activity, by using --no-probe-filter on the command line.
Products: Visium for FFPE