[galaxy-user] Problem with repeated genes in Cuffdiff's output

Hi all, I am working on RNA-seq using TopHat/Cufflink/Cuffdiff for differential gene expression and new gene discovery ( this is what I am interested in). However, I found many genes that are repeated in the Cuffdiff's ouput. These are the same genes and at the exact the same locus. There should be only one gene for 1 line. Something like this: *Genes* *Locus* *Status* *q1* *q2* *Log2 Folg change* *Significance* * Lnp* *2:74517521-74584544* *OK* *8.91501* *85.2735* *3.25779* * yes* *Lnp * *2:74517521-74584544* *OK* *12.0044* *171.352* *3.83533* * yes*

If I re-run the Cuffdiff for differential gene expression only ( No gene discovery), the problem is fixed. Anyone knows how o explain and fix this? Thank you so much