Discovery of novel transcripts in multiple experiments

[profkaramba]

Hi everyone

I have 100 RNA-seq sets from 100 human individuals (diseased and controls).
I would like to discovery novel transcripts (especially ones that are only expressed in diseased individuals). What is the best approach?

1) run 100 times stringTie and then merge?
2) merge the 100 BAMs and run stringTie (if it's possible to run it...)
3) other?

I would like to optimize the discovery of lowly expressed transcripts.
Do you have any idea? All feedback is welcome.

Thank you very much