The 4DN ChIP-seq data processing pipeline uses the ENCODE ChIP-seq pipeline v1.1.1. We have modified the logistics of the pipeline execution without changing the content of the pipeline.
We have split the pipeline into three sub-pipelines; 1) alignment and filtering for ChIP, 2) alignment and filtering for control input, and 3) peak calling. Quality control report is generated at each step.
For more detail, see description/documentation from ENCODE