Im using stringTie to assemble the transcripts using my genome annotation file with -G flag. but stringTie assigns its own IDs like MSTRG .1, MSTRG.2 to genes and MSTRG1.1 and MSTRG 2,1 to transcripts despite of using geneom annotation file and im unable to get same gene IDs as to that in genome annotation file. I need those IDs for subsequent functional analysis. Can anyone suggest me how to get the same IDs in stringtie output as to that in genome annotation file????
thanks in anticipation