compare kallisto-bustools and cellranger for single nuclei sequencing data

In my last post, I tried to include transgenes to the cellranger reference and want to get the counts for the transgenes. However, even after I extended the Tdtomato and Cre with the potential 3’UTR, I still get very few cells express them. This is confusing to me.

My next thought is: maybe the STAR aligner is doing something weird that excluded those reads? At this point, I want to give kb-python< …