transcripts id to gene id

[knert]

HI, 

Thank you for your convenient tool for RNA seq analysis. 

I have one question when analyzing my fruitfly data. 

When I converted the transcripts id to gene id obtained from  the excel file" Significant DTU transcripts list and statistics", I found that did not match the column of "Genes of DTU transcripts" in excel file "Gene list of 3D genes and transcripts" downloaded from the functional analysis page. 

I used flymine to convert the FBtr to FBgn. 

Which causes this difference?

Thank you for your help

Best, 

knert