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rnaseq / degraTrans

RNA-seq performances in the context of degraded transcriptome annotations.
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RNA-seq: read simulation #4

Open rnaseq opened 8 years ago

rnaseq commented 8 years ago

Select RNA-seq simulation: software e.g FluxSimulator, RSEM etc. Select RNA-seq simulation: parameters.

Add to the discussion: which simulator(s) to use (1 or many) and how the simulator(s) used for generating the data affect(s) the results.

mw55309 commented 8 years ago

Hey @rob-p any movement on read simulation? You have previously suggested RSEM and/or flux simulator

rob-p commented 8 years ago

Ok, I have a fairly substantial update to the plan here. There have recently been some substantial improvements made to the efficiency of Polyester that now make it possible to simulate datasets over the entire genome in reasonable time. Given the other benefits of Polyester, I think this makes it a potentially better choice than Flux or RSEM Sim — e.g. we can bake transcript-level DE directly into the simulation, and then validate not only on abundance estimates but also the effect on downstream differential analysis.