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Old 04-30-2010, 02:45 AM   #5
ymc
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Location: Hong Kong

Join Date: Mar 2010
Posts: 498
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Quote:
Originally Posted by Gianza View Post
Hello everybody,
I'm struggling with the same problem.
I'm on the way to buy a desktop/workstation.
My project is the following- eukaryote-plant
-454 EST assembly 1,5 M reads from 3 different samples (for SNP mining)
Looking to use MIRA, the extimated memory usage is 8 Gb. OK
-Solexa reads (always from cDNA) mapping to reference sequence (generated
by 454) ; aprox. 30 M reads to map (always for SNP mining on other
samples).For this one I'm looking to use MOSAIK (MIRA gave me an exitation
of memory around 30 Gb).

The question is the following:
Does a desktop/workstation with a quad-core (intel i7 860) with 12 Gb can handle this kind of Solexa mapping, or, any scripts will run out of memory??
I'm also considering to install 24 Gb instead of 12 Gb but I cannot understand if this might be crucial or just wasted money (because there is no way to run a Solexa mapping without a powerful cluster).
I mean, I don't care if the assembly will take one or two days; but I just wanna make sure it will be accomplished without crashing. In other word, having a cluster with 256 Gb of RAM, is just a matter of run time or it is the pivotal point to avoid the assembler to crash?

Can anyone give me some highlight on what I should expect from such a machine I'm planning to buy.

Thanks, I will appriciate.

Davide
You can also buy two 15K RPM SAS drives or two WD 10K SATA drives to form RAID0 for the swap memory. You can try this before you spend big money on the RAM.
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