ENCODE ChIP-seq pipeline2

Identifier: WF_dd6938.8f


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.

Job Costs*

Costs for this workflow can vary widely. Primary determinants of cost include the number of samples (multiple can be specified in a single job), input file sizes, number of controls, and what options are chosen (workflow can only do alignment step, xcor, etc.).


Public example Job cost Notes
ENCSR135FYV Control ChIP-seq alignonly $ 12 This is a control sample that only does alignment. (No peak calling)
Re-run of ENCODE ChIP-seq analysis ENCSR777VNA $ 45 This is a SE mouse sample with 2 samples and 2 controls.
ENCODE ChIP-seq analysis ENCSR859FDL $ 96 This is a PE human cell line sample with 2 biological replicates and 2 controls.

*Job cost examples are for estimates only. To get a more accurate idea of job costs, try running a single job before running many jobs.

Code Repository
  • GitHub


Tutorial Videos