Question: What is the difference between Promoter Sum, and Nearby Gene Sum in Loupe Browser?
Answer: Here are the definitions of these two feature types:
Promoter Sum: For a given gene, the promoter sum is the number of cut sites per cell that fall within all the peaks labeled as promoters for that gene (1,000 bases upstream from a gene's transcription start site, or 100 bases downstream from a gene's transcription start site).
Nearby Gene Sum: The number of cut sites per cell that fall within that gene's promoter and distal peaks. Any peaks within 200kb of a genes's TSS is considered to be associated with that gene.
Products: Single Cell Multiome, Single Cell ATAC