I am confused slightly with the results I am getting from the stringtie merged file output. I have one entry called: MSTRG.13580.
In the stringtie merged GTF file output, it has the 2 following separate entries
Entry 1: gene_id "MSTRG.13580"; transcript_id "MSTRG.13580.1"; -> with coordinates on chr19, 52415921 - 52426291
Entry 2: gene_id "MSTRG.13580"; transcript_id "ENST00000359924"; gene_name "BBC3"; ref_gene_id "ENSG00000105327"; -> with coordinates on chr19 52415924 - 52426291.
I wonder why entry no 1 is not given the gene name BBC3, while entry no 2 is given BBC3? Arent they supposedly from the same gene since the 2 entries have the same MSTRG no of 13580? Does this have to do with the 3 base pair difference (in bold) in chromosomal location of the two transcripts?