Basically, there are 2 steps
- The identification of the transcripts.
- Estimating the "relative" abundance of those transcripts in your sample.
When you say you have already have isoforms in hand, I believe that you are already done with the step#1.
So, if you have the bam files and the corresponding reference genome in hand, you can run stringtie to estimate the abundances (step#2)
In case if you are not yet done with step#1 then you will have to run stringtie 2 times as described below
- first time with the bam files and the reference file to perform a "reference guided" transcriptome assembly.
- taking the consensus set of transcripts from all samples as reference, you will have to estimate their abundance.
By abundance, I mean the FPKM or TPM values (or your favourite metric) which stringtie will generate for you.
NOTE: StringTie is part of the new tuxedo protocol.