Computer build for small core lab

Question

[emilyblake0202]

I'm putting together computer specs for a new small core lab, and I am between the HP Z840 and the Dell Precision Tower 7000 series. Does anyone have a preference for one versus the other when it comes to analysis for RNA-seq, genome, and methylation-seq analysis (no de novo)? I will be the only user of this workstation, and I will have access to additional server storage space. Current project load is 6 RNA-seq projects and 1 methylation-seq project.

I would really appreciate feedback on the following build from members that routinely run human/mouse RNA-seq analysis:

Dell Precision Tower 7810
-Intel® Xeon® Processor E5-2660 v4 (14C, 2.0GHz, 3.2GHz Turbo, 2400MHz, 35MB, 105W)...do I need more cores?
-Red Hat Enterprise Linux WS v7.2...is Ubuntu preferable?
-NVIDIA® Quadro® K620 2GB (DP, DL-DVI-I) (1 DP to SL-DVI adapter)...is this overkill or should I stick with the standard AMD GPU?
-128GB (4x32GB) 2400MHz DDR4 RDIMM ECC...can I get by with 64GB?
-Internal Hard Drive Configuration: C2 SATA / SSD 3.5 Inch, 3 Hard Drives (Integrated Controller)
-Hard Drive: 4TB 3.5" Serial-ATA (5,400 RPM) Hard Drive
-2nd Hard Drive: 2TB 3.5" Serial-ATA (7,200 RPM) Hard Drive
-3rd Hard Drive: 2TB 3.5" Serial-ATA (7,200 RPM) Hard Drive

[GenoMax]

Subtract the GPU, get a basic graphics adapter. Use that money to get an SSD (512G should be enough) for the system drive. Keep the RAM at 128. There is no substitute for real RAM down the road.

HP/Dell choice should be dependent on which vendor your local institution has the best business relationship/experience with. Either vendor would be fine.

Answer 1

[dyollluap]

-Intel® Xeon® Processor E5-2660 v4 (14C, 2.0GHz, 3.2GHz Turbo, 2400MHz, 35MB, 105W)...do I need more cores?

• More cores are good if you're using tools that can be optimized with multi-thread operations, or batch processing... I run QC across as many cores as I have available.

-Red Hat Enterprise Linux WS v7.2...is Ubuntu preferable?

• I've used both, no preference/opinion.

-NVIDIA® Quadro® K620 2GB (DP, DL-DVI-I) (1 DP to SL-DVI adapter)...is this overkill or should I stick with the standard AMD GPU?

• Yes overkill for RNA-seq analysis

-128GB (4x32GB) 2400MHz DDR4 RDIMM ECC...can I get by with 64GB?

• More is better

-Internal Hard Drive Configuration: C2 SATA / SSD 3.5 Inch, 3 Hard Drives (Integrated Controller) -Hard Drive: 4TB 3.5" Serial-ATA (5,400 RPM) Hard Drive -2nd Hard Drive: 2TB 3.5" Serial-ATA (7,200 RPM) Hard Drive -3rd Hard Drive: 2TB 3.5" Serial-ATA (7,200 RPM) Hard Drive

• If you can get an SSD to run analysis on and the 2nd/3rd HD for staging data you're going to get a lot better resource value than a high end GPU. Makes it so much faster moving data around with alignments and processing. It's also beneficial moving large files around when paired with usb3 or gigabit ethernet.