How to evaluate the RNA-Seq analysis software I choose?

[Huijuan]

Hi,I am a newbie here, I want to get familiar with the RNA-Seq pipeline and so I choose several softwares in each step like Bowtie,BWA,TopHat with mapping and DEGseq,Cufflinks with DE analysis.But the point is that how to evaluate the results from the combination of softwares in each step,what index can be used to evaluate them ,should I generate some simulated data or something? I am totally confused.
Thank you for your time ~~

[Simon Anders]

See, e.g., this thread: http://seqanswers.com/forums/showthread.php?t=10797 (and fotr my 2 cents on why simulation doesn't help, see my post #6.)