I'm curious if anyone has any experience simulating RNA-seq reads for aligner comparisons? I've found a software package called flux simulator that supposedly will do this. But I was hoping to hear if anyone has any thoughts on it? or if anyone has used a different method?
I googled "rna-seq simulation" and this page was the first hit. They mention FluxSimulator and a tool called dwgsim from the dnaa package and another tool from maq. I have never used these tools before, though, so I can't offer much perspective. However, I do know that a student in my last research group ended up rolling his own from scratch after not finding something suitable.
I'm not against simulation: I think it's very important and will become increasingly important in the future. But I also agree with the comments on the linked thread suggesting they download real data as well. There are so many hidden layers of information that we will never be able to simulate accurately. Just something to keep in mind.