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Old 01-23-2014, 12:52 PM   #1
Parharn
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Default Computer specs for RNA-seq S.pombe

Hi all,
I am thinking to buy a workstation/desktop for purpose of analyzing RNA-seq data for s.pombe. I have around 20 million reads in each sample and need to run tophat and cufflink for analysis. What are your suggestions? Main things i like to know is the CPU, RAM, motherboard and hard disk. Of course any other suggestions are much appreciated. Please be specific about the brand names, speed and any specs of pieces. To my knowledge it is very important to know what pieces to assemble together so they will work at their highest performance.

Thanks,
Parham
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Old 01-23-2014, 01:22 PM   #2
TompaB
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I'm in a very similar situation. I have started off trying to find a good value for money workstation and building from that. I know that there are different thoughts on this, some go for a decent number-cruncher server, single instance with dual CPUs and many cores, others go for clusters et.c. My thought is to build on a high spec workstation. The reason for me is that it has never been wise to try to buy computer power to last. Thus, I'm aiming for a workstation with the best value performance processors right now for what I need this minute and can then feel in a year or so that I can move this workstation on to other duties in my lab and purchase a new one. With such approach I find that I can halve the price roughly.

The specs I'm looking at currently is an HP Z820 with two 6-core Xeon E5-2630 v2 (2.6-3.1 GHz) CPUs and 64-96 GB ECC RAM (1600 MHz, the 1866 MHz is too expensive). The Extra memory is because we are running STAR. To this, I'm adding an 256SSD for OS and and RAID array after market. Such a setup is around €3000

You can probably by something in individual components and assemble it yourself, but with this I know everything will work together well, the build quality of the Z820 is really good and you get 3-year on-site warranty.

Good to hear other comments, as I'm about to purchase this system really soon...
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Old 01-23-2014, 01:43 PM   #3
Parharn
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Thanks for your thorough response. Well I guess I don't need that powerful machine, since s.pombe genome is small and I managed to do initial data analysis with an ordinary office desktop. The desktop has a i5-3470 3.20 GHz Intel cpu and 8GB RAM. I am not sure if i was short in CPU or RAM for aligning seqs. However my guess is that RAM issue comes in first then it is CPU, or am I wrong? So would expanding RAM to 16 or 32 be enough or I really need a more powerful CPU?
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Old 01-23-2014, 02:23 PM   #4
GenoMax
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You are on right track. Get some more RAM (32 would be nice but 16 may be enough for pombe if that is all you will ever analyze). Having a less powerful CPU just adds to the computational time needed but if you run out of RAM there is no substitute. If you do decide to move up to a better CPU/MB combination in future then you would be able to re-use the RAM.
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Old 01-24-2014, 04:23 AM   #5
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Yes, I think I will do that. Thanks!
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Old 01-24-2014, 05:26 AM   #6
biznatch
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I've aligned ~50 million mouse RNA-seq reads on my 2 year old laptop (i7, 16GB RAM). It had to run overnight but it worked. So you shouldn't need something that powerful for only 20 million sequences and a smaller genome.

If you're using Tophat (ie. Bowtie) to do the alignment than more RAM won't speed it up. I'm pretty sure it just needs enough RAM to hold the genome index in memory and that only takes a few GB. 16 GB should be plenty of RAM for this kind of thing, I think it would even work with 8. I do ChIP-seq and RNA-seq and the only thing I've needed more than 16GB of RAM for is to run wigToBigWig on the entire mouse genome (that takes ~31GB btw). More cores on your CPU or a faster CPU will speed up the alignment though because a lot of the alignment is multi-threaded. Anyways, adding more RAM in the future is pretty easy while upgrading a CPU is more work. So get a good CPU now but I wouldn't go crazy with tons of RAM until you find you actually need it.

For hard drives I'd get a WD 2-3TB Black drive to start and make sure whatever computer you are setting up has room for adding a few more drives if needed in the future. Also you'll need some kind of backup system, maybe external hard drives. If you want, you could setup the OS and programs on a ~120GB SSD.

Last edited by biznatch; 01-24-2014 at 05:35 AM.
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Old 01-24-2014, 05:51 AM   #7
Parharn
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Yes biznatch, I was about to come to the same conclusion by reading about the computer specs for these kind of analysis. You made me more certain about the decision! Thanks a lot!
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Old 01-24-2014, 05:53 AM   #8
Parharn
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Do you have any opinion on motherboards? Asus, dell, lenovo or any other?
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Old 01-24-2014, 06:06 AM   #9
GenoMax
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If you are the sole user of this workstation then whatever fits your budget (and which ever company has the best local support in case of problems) should be fine.

If you intend to provide access to this hardware as a service then you would want to think about an enterprise vendor.

There are any number of hardware review sites on the net. Check http://www.anandtech.com/ which is a well-respected site for in-depth hardware reviews. They also have an editor who covers enterprise computing.

Last edited by GenoMax; 01-24-2014 at 06:14 AM.
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