I try to setup a Iontorrent RNA-seq simulation experiment. Following the help and our owns protocols I success creating one experiment with Flux simulator.
Things is I want to setup a differential expression simulation. I want two experiments and a file summarising the difference between both experiments (for example RPKM). I cannot find a way to simulate this. Could I make it works with Flux-simulator?
the degree of differential expression varies depending whether the two states you compare are different tissues, cell types, or merely a modification of the state of a cell (e.g., change of nutrition, drug treatment, etc.). According to the degree of changes you expect, you might wish to derive a second .PRO file from a simulated expression profile by your own models, or you re-run the expression simulation to obtain a completely different profile.
As you say you are focusing on the Iontorrent platform, where specific sequencing models have not yet been implemented in the simulation pipeline, although this is certainly possible. Please let us know if you have data to estimate the error model of your machine.