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.

I was just wondering if anyone has a good way of running DEXSeq on such a
large cohort. Tips on how to reduce run time? Are there way to parallelize
these jobs across a cluster rather than rely on a single machine with
multi-cores? Any help would be greatly appreciated.

Thanks,

Fong

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