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What is Total Transcripts?

Total Transcripts is the sum of all detected transcript molecules across every gene in the dataset.

In spatial gene expression data, each sequenced mRNA molecule captured at a spatial location is counted as one transcript. The total transcript count is computed by summing the raw gene counts (gn) across all genes in the gene count file.

  • What it measures: the overall sequencing depth of the dataset — how many mRNA molecules were detected in total
  • Where it appears: in the ROI drawer, shown alongside the number of ROIs as dataset-level context

Tips

This value reflects the full dataset, not just the currently visible map area or selected ROI.