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MonashBioinformaticsPlatform / polyApipe

polyApipe
GNU Lesser General Public License v2.1
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quantifying pre-defined poly(A) sites #8

Open CharlotteAnne opened 1 month ago

CharlotteAnne commented 1 month ago

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 commented 1 month ago

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.