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(2012) ENCODE: TF ChIP-seq peak calling using the Irreproducibility Discovery Rate (IDR) framework

Last Updated: Oct 2, 2017

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Latest pipeline

We recommend using the latest stable ENCODE AQUAS ChIP-seq processing pipeline at

This google doc exposes all the individual commands using in the pipeline code. 

The pipeline is the official specification for the ENCODE TF ChIP-seq processing pipeline.

Deprecated older pipeline (2012 version)

For posterity only (Not recommended and not maintained)