How to validate RNAseq pipeline

[biofreak]

Hi
I have created a pipeline to process RNAseq data and have used DEseq to conduct differential expression analysis. The question is, how do I know it is giving valid results? Are there any gold standard datasets with which I can compare my results?
thanks

[Mchicken]

One possibility would be the Flux simulator, which is simulating RNA-Seq experiments. In the .pro file you can see the actual amount of transcripts in your transcriptome, the number of produced fragments from the transcripts as well as the number of reads produced from each transcript. You could then analyze the simulated fastq-file with your pipeline and compare your findings to the values in the .pro file.