I wanted to rerun my DGE analysis to see if there were any differences between HTseq-count -> edgeR and StringTie-Ballgown.
However, when I tried to run my stringtie command using the same BAM file, I got an error: "Error: no valid ID found for GFF record"
I think I read somewhere that Stringtie only likes Ensembl gtfs, I was wondering if one of you can confirm this. My previous DGE analysis was performed using reference genome from NCBI.
There is a way to delete posts, but there is no need to do it. Just because you found the solution doesn't mean this stops being a problem for others. Instead, your posted solution will help others when they search the archives with a similar problem.