Simulating Rna-Seq Reads

Question

[Gww]

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?

[H.Hasani]

After almost 6 years from your thread. Could you please share what was the tool you used and your experience?

Answer 1

[Daniel Standage]

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.

[Gww]

Thanks for the comments, I am more interested in checking the aligners sensitivity for predicting novel splice junctions so I was hoping for some suggestions on simulating reads with those. At least with those sets I can have an idea of what the novel junctions are supposed to be. If I use a real datasets I don't know those for sure.

Answer 2

[biobot 0.0.77.a.1099]

See these answers. Not mentioned in those answers, the RSEM package provides a simulation facility (I've only read the paper, I haven't used the software yet).

[Gww]

Thanks for the link about the RSEM package I will definitely check that out.