Multi-occurence of transcripts in Cufflinks output file

[Jesse K.]

Dear all,

although I'm new to the analysis of RNA-seq data, I finally managed to align my reads with STAR and afterwards calculated transcript abundances with Cufflinks. As I checked the isoforms.fpkm_tracking file, I realized that the tracking ids are not unique. How can it be, that I have some tracking ids occur so often? (I used for both, STAR and Cufflinks, an annotation file with Ensembl Ids)

Regards,
Jesse