I face a problem like I get Different ENSG IDs for the same MSTRG IDs. I used StringTie as the assembler but at the * StringTie_merged.gtf * file I get this problem that I have same MSTRG ID for genes that have a different name and different ENSG IDs. Does it seem that StringTie gives same MSTRG ID for those genes which overlap? How can I solve this problem?
Thank you in Advance.