Hi,

Most people using the RNA-Seq toolkit use a combination of Tophat/Cufflinks/Cuffdiff. A known issue is that cufflinks and cuffdiff use different normalisation schemes (http://seqanswers.com/forums/archive/index.php/t-26041.html). Users overcome this problem by running cufflinks with the following flags:

--compatible-hits-norm --max-frag-multihits 1