Building a compute server for RNA-seq

[moldoverb]

Hi all,

I'm going to be processing a number of Illumina paired-end RNA-seq samples, and looking to build a new server to handle the load. Production work can be done on a cluster once we get going (over 2k samples planned) but for now I want something I can use for 6-20 samples over the next couple months.

I was thinking of something with 8 cores, 32gb memory, but more cores would be better. Any suggestions on what would be an ideal configuration, even down to specifying hardware, would be appreciated

[GenoMax]

Here is a thread about this from not so long ago. 6-20 samples over a couple of months can be done on a very simple *nix machine.

http://seqanswers.com/forums/showthread.php?t=24772

If you are planning to move to a cluster eventually why not just start there?

[moldoverb]

Here is a thread about this from not so long ago. 6-20 samples over a couple of months can be done on a very simple *nix machine.

http://seqanswers.com/forums/showthread.php?t=24772

Thanks. A lot of that thread is geared toward buying Apple. I plan on building a server. Also the CPU's they recommend are $1500 each. No discussion of AMD as an alternative.

[GenoMax]

Thanks. A lot of that thread is geared toward buying Apple. I plan on building a server. Also the CPU's they recommend are $1500 each. No discussion of AMD as an alternative.

Posts #6 and #4 have the general info you are looking for in that thread. Since linux will run equally well on intel or AMD chips the exact CPU purchase would be your choice.

[moldoverb]

Posts #6 and #4 have the general info you are looking for in that thread. Since linux will run equally well on intel or AMD chips the exact CPU purchase would be your choice.

Looking at the AMD 6273 processor - 16 cores and I could put two on one motherboard. Only issue is that it is limited to 8 FPU's and I don't know if tophat/cufflinks etc. does a lot of floating-point calculations or mostly integer.

[turnersd]

I might interject opting for 48GB RAM instead of 32. I bet you'll see newer aligners (e.g. STAR) come out over the next few years that trade a modest memory requirement increase for a big gain in mapping speed. STAR requires about 30GB RAM. 32 might be insufficient after any OS and other requirements.

[moldoverb]

This is getting fun. It looks like I could build a decent machine for around $2200. I have a 4Tb RAID array which I can dedicate to this machine, and a couple 1Tb drives, so that saves money. To turnersd point, I can always add more memory later.

2x AMD Opteron 6272 CPU (16 core each)
32gb Quad memory
256gb SSD

cooling/case/DVD