Question: DEXSeq: How to reduce compute time for estimating dispersions for large datasets.
gravatar for mjrarcher
10 months ago by
mjrarcher0 wrote:


I am using DEXSeq to infer differential exon usage across 3 conditions for over 100 samples each with more than 500,000 exons.

After estimating size factors, the estimatedispersion step is taking quite a long time to complete. I'm running it on 32 cores and have dedicated a 100 GB of memory, but after 15 hours, its barely made any progress and is at 13%.

I read on an older post from Alejandro to use a former TRT implementation, but apparently that is now no longer in use. 

Is there any way around this issue? Appreciate any suggestions.



ADD COMMENTlink written 10 months ago by mjrarcher0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 438 users visited in the last hour