I am following a pipeline to extract new variants for A. thaliana. I have already conducted this part of the process but I am doing it again with a newer annotation.gtf to improve and actualize results.
However, the structure of that new .gtf is slightly different, and I am facing errors while running stringtie.
I don't really have clue about how to "resolve" it, or if that is really an issue?
Here is the command I execute : $ stringtie --rf -G ../files/Arabidopsis.gtf -o myFolder myfile.bam
Here are the errors I get :
So here are the corresponding structures of :
the result of the stringtie construction:
Perhaps I am wrong, but I don't really see any discard of information here? Hope someone had to face the problem, thanks in advance!