zhou-ran / singlecellapa_evaluation Goto Github PK

Hello, I have some confusion about the output of SCAPE, and I am not quite sure what the "count" in the pasite.csv.gz file refers to:

1:40004:36:+,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,2,0,0,1,0,1,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

May I know what do these values represent?

Hi, Ran.
I used psiCategory.R to calculate the psi values for pA sites, but I thought it would calculate the psi values for genes. In your article, "Category of pA usage" mentions, "To better understand the heterogeneity of APA patterns among cell populations, we first calculated the usage of pA sites for each gene at single cell level." Is this categorization for genes or for pA sites?
Regarding the section on "Expected pA length," is the calculated value referring to the usage of a single pA site or the usage of pA sites within a gene?
thank you very much!