I was using Cufflinks to analyze Clip-Seq data. The results as 'gene expression' and 'transcript expression' gave me almost same results (No. of genes ? No. of transcripts). I guess the number of genes should be relatively smaller than that in transcripts. I wonder if I need to get a special format for the annotation? I used '62: UCSC Main on Human: refGene (genome)'. Thanks, Songyan Liu