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.
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.
- Encode Project Website