[BioC] Efficiently running DEXSeq for Large Cohorts

[Steve Lianoglou]

Hi,

On Mon, Jan 14, 2013 at 3:57 AM, Fong Chun Chan <fongchun at alumni.ubc.ca> wrote:
> Hi all,
>
> I've been trying to get DEXSeq to run on a fairly large RNA-seq cohort that
> I have. To be specific, I have 89 samples and I am attempt to generate DE
> exon usage results on > 500,000 exons.
>
> I've followed the latest tutorial (1.5.6) on Bioconductor and it so far
> I've had relatively no problems. It just the two steps that are mentioned,
> estimateDispersions and testForDEU, are taking a fairly long time. I've
> already attempted to parallelize this on a 48-core 256GB machine, but I get
> very little progress on the run-time of these functions.

If you look at the cpu usage of your machine -- on linux you might us
`top` or `htop`, for instance -- are all 48 cores typically pegged at
100% usage?

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact