I've used Hisat-StringTie-ballgown pipeline and Using mouse genome 91 gtf file from ensemble creates MSTRG values as partial output of Stringtie,
The number of those MSTRG can be high, and I'm not sure is a real, as too many new transcripts, or unassembled transcripts.
Is there a different way to do it to avoid this probably technical issue? Using a different assembler?
Or a different gtf file?
This issue has been raised before, however, no good answer was provided: Gene names in Ballgown differential expression analysis How to deal with MSTRG tag without relevant gene name? Converting MSTRG from stringtie with gene name https://stackoverflow.com/questions/47621574/search-and-replace-between-two-files-post2