ENCODE ChIP-seq pipeline2
Version:v1.6.0
Identifier: WF_dd6938.8f
Workflow
Description
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.).
Examples:
| 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.
Links
- Encode Project Website
https://www.encodeproject.org/data-standards/chip-seq/
- GitHub
https://github.com/ENCODE-DCC/chip-seq-pipeline2/
- ChIP-seq demo
https://www.youtube.com/watch?v=eSwtF1t3uCw