quantifying pre-defined poly(A) sites

[CharlotteAnne]

Hiya! Came here from the seurat PASTA code - is there a way to provide your own GTF to this pipeline for quantification rather than determining the poly(A) sites de novo?
Cheers!
Charlotte

[pfh]

Hi Charlotte,

There isn't currently a way to specify your own set of sites. Also development of polyApipe is on hiatus at the moment, and it's not in a very usable state. If you get to the point of have counts per cell x site, the weitrix package might provide a useful statistical method.

Thanks for telling me about PASTA.