I have single-cell data with wild type and knock-out gene A. When I open the loupe file of both wild type and knock-out, I can find gene A in both samples. However, when I use
Findallmarker() on the Seurat object from wild type, I don't find gene A, even after setting
logfc.threshold = 0 and
minpct = 0.1. This made me very confused. Gene A should show in the wild type sample. Would you please have a suggestion? Sorry but I don't know anyone else to ask.