very large datasets

[Hunter Richards]

Hi Anton,

Do you have any recommendations for analyzing very large datasets with QuEST? I'm running a set with about 75 million ChIP and 220 million input reads. I maxed out my 24GB of RAM so I created a 30GB swap and it's using about 18GB of that (total of 42GB of memory). I could upgrade the RAM but that'll cost at least $1200.

Anything that allows QuEST to run on less RAM?

Thanks,

-hunter

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Hunter Richards
Postdoctoral Scientist
Department of Genome Dynamics
Lawrence Berkeley National Laboratory
1 Cyclotron Rd, Bldg 977-138
University of California, Berkeley, 94720
510-486-4663

[Anton]

Hi Hunter, the RAM shouldn't matter as long as the swap is big enough. So, when you have 16 Gb of RAM, all you need is a big enough drive for the swap.

We actually ran QuEST on a 2003 Mac with 1 Gb of RAM. It was slow, but it did work.

[Hunter Richards]

Yeah, the 30GB swap I would up using was enough, but it was slow; it took about 30 minutes just to load the control file, and the swap was on an SSD drive.

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