Question: What does “Genome Sum” mean in Loupe Browser?
Answer: Since cellranger v3.0, a new aggregate feature sum has been added in the
.cloupe file. “Genome Sum” is one of the aggregate feature sums (left panel of the figure below), which shows the total UMI counts of all genes listed in the GTF file. The feature name is determined by the
--genome flag during
cellranger mkref pipeline. Here, since the command line
cellranger mkref --genome=GRCh38 ... was used during reference generation, the feature name of “Genome Sum” adopts
--genome argument and shows as “GRCh38 sum”.
This "Genome Sum" feature enables the visualization of UMI sums of all genes per cell in UMAP/t-SNE plot (or Feature Plot). It could be useful to visualize low-quality cells or multiplets with very low or high UMI counts respectively.
In addition to “Genome Sum”, there are other types of aggregate feature sums, such as the total number of cell surface markers detected per cell (right panel of the figure below). Users can type “Sum” into autocomplete search bar in the “Gene/Feature Expression” panel to explore this feature.