Cuffdiff2 Gene Level Quantification

Question

[narges]

Hi,

I wanted to ask if any one knows how cuffdiff2 calculate the gene level quantification if the intention of study is detecting DE genes but not DE transcripts. So, I have provided a genome reference for cuffdiff2 and done the DE analysis. Based on the paper (http://cbio.ensmp.fr/~jvert/svn/bibli/local/Trapnell2012Differential.pdf), it should first quantify the transcript levels and then sum up the transcript levels related to a gene to obtain gene level expression. But in this case should nt I provide a transcriptome reference for it instead of genome reference? Thank you in advance