So following the updated STAR alignment with the updated gff3 file for the Acer CCC samples, I re-tried the code from Natalia and got different results which I think means it worked!

Before:

After:

So that means the gene IDs worked, which is good. I haven’t tried the stringtie pipeline to see if the MSTRG things come up. I could just continue on with Natalia’s pipeline, at least for the Acer ones and see if I get DEGs with that.

I see now though that I also did the stringtie for Acer CCC on the original samples (not with this newest updated gff3), so maybe I could try that and then compare the gene matrices.