Is it possible to rerun an encode pipeline?

Question

[ivar.grytten]

Assume I want to reproduce the results from an encode exeriment (e.g. this: https://www.encodeproject.org/experiments/ENCSR000EIY/), is that possible?

I know it is possible using dnanexus.com 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. https://github.com/ENCODE-DCC/dnase_pipeline), but how do I run this pipeline for one specific experiment?

[Santosh Anand]

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

http://scofield.bx.psu.edu/~dannon/encodevm/

https://www.encodeproject.org/about/2012-integrative-analysis/

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 ....

Answer 1

[ivar.grytten]

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

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

https://github.com/kundajelab/atac_dnase_pipelines

Quote from github repo:

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

[Jeremy Leipzig]

Truwl.com has this pipeline as a runnable workflow