README.md

ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline

This ChIP-Seq pipeline is based off the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline specifications (by Anshul Kundaje) in this google doc.

Installation / Tutorial

• Google Cloud Platform
• DNANexus Platform with dxWDL CLI
• DNANexus Platform with Web UI
• Stanford SCG
• Stanford Sherlock 2.0
• SLURM
• Sun GridEngine (SGE)
• Local system with singularity
• Local system with docker
• Local system with Conda

Input JSON

Output