Question: Is it possible to rerun an encode pipeline?
gravatar for ivar.grytten
3.6 years ago by
ivar.grytten40 wrote:

Assume I want to reproduce the results from an encode exeriment (e.g. this:, is that possible?

I know it is possible using service, but is this possible to do it without using dnanexus?

It seems that the data from each experiment is generated by running an encode pipeline (e.g., but how do I run this pipeline for one specific experiment?

alignment encode • 1.1k views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 3.6 years ago by ivar.grytten40

Encode also published VM for reproducible results, if that can be of any help

PS: I am afraid that you won't be able to get the same results as "ENCODE Uniform Processing Pipeline (EUPP)". By definition, the EUPP processed all the data uniformly (and perhaps simultaneously) over all samples, which might be different from processing a single sample. Just a guess, however ....

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Santosh Anand5.1k
gravatar for ivar.grytten
3.5 years ago by
ivar.grytten40 wrote:

After searching around a lot, I've concluded that Encode does not let you reproduce their pipelines without using

However, I found this that works for the atac seq pipeline:

Quote from github repo:

The ATAC-seq pipeline specification is also the official pipeline specification of the Encyclopedia of DNA Elements (ENCODE) consortium.

ADD COMMENTlink written 3.5 years ago by ivar.grytten40
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