RNA Seq Hardware Options

[S89A]

I am planning on running routine de novo analysis of RNA data using SeqMan-NGEN. The miniumum hardware requirements have been stated many times, I am hoping that my questions are specific enough to warrent their own thread.

Regarding my RNA Seq workstation I would like some opinion regarding the following:

Would I be better with a 2 x Xeon X5650 (Hex Core) or a 2 x XEON X5680 (quad core) processor?

I know RAM is crucial especially for de novo assembly but would I notice much improvement if i opted for 96 GB rather than 64 GB?

Thanks in advance for any help...

[GenoMax]

It is difficult to provide a definitive answer for your questions. Unless the programs you are planning to run are multi-threaded having more cores will not help. Even if the programs are multi-threaded having 4 more cores may cut time off the length of a run (but not make a difference as to whether you can run that program or not). RAM on the other hand may be crucial since not having enough RAM would make a program not run.

Depending on how the cost dynamics are working in this case I would suggest that you opt for the most RAM you can afford, even if that means going to a slower/lesser CPU. Having more RAM would not necessarily make programs run faster, just to set the right expectation.