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

Contents 1 Mailing List 2 Latest pipeline 3 Deprecated older pipeline (2012 version) Last Updated: Oct 2, 2017 Mailing List Please join the IDR mailing list https://groups.google.com/group/idr-discuss for FAQs, discussions and updates on software. Latest pipeline We recommend using the latest stable ENCODE AQUAS ChIP-seq processing pipeline at https://github.com/ENCODE-DCC/chip-seq-pipeline2 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) https://sites.google.com/site/anshulkundaje/projects/idr/deprecated

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