It seems to me that cufflinks is taking long time to assemble the transcript, but I have tested the same transcript with StringTie it taking fraction of what cufflinks is taking. So my question is it good to use StringTie and then use the output for downstream tuxedo protocol analysis or I have keep the tuxedo protocol intact .would it make a difference in the final result if I use stringTie , I suppose it will but how drastic would it be?

Any suggestion or help would be highly appreciated