I was wondering how to find novel transcripts under different treatment conditions using stringTie?
I have 4 different treatments and 3 replications for each of the treatments in my RNAseq data. I have tried to merge the 12 gtf files generated by stringTie and compared the merged gtf to the reference gtf file using gffcompare. However, I am not sure what I should do if I would like to find out novel transcripts in different treatments. Should I combine the gtf files from the 3 replications for each treatment, and compare the combined gtf to reference gtf file? How can I make a comparison across the 4 different treatments? Does that make the question into finding out DEGs between different treatments?
Hope my silly questions make sense.
Thank you for your attention and help!