I have the same bam files from TopHat and I have used both cuffidd and HTseq(and then R package) to get DE genes. The problem is that the number of genes are not the same in HTseq and cuffdiff. I was expected not to get same number of counts for each gene but not same number of genes as the reference has been the same for both. I have more number of genes in HTseq output than in cuffdiff. Any idea about the reason would be appreciated.