========== ENCODE ChIP-seq Pipeline
ENCODE Uniform processing pipeline for ChIP-seq
Current implementation is deployed to the DNAnexus platform.
- Map reads with BWA, mark duplicates Picard, and remove duplicates.
- Estimate library complexity and calculate calculate NRF (non-redundant fraction), PBC1, PBC2 (PCR bottleneck coefficient).
- Calculate cross-correlation analysis with spp/phantompeakqualtools.
- Generate p-value and fold-over-control signal tracks for each replicate and replicates pooled with MACS2.
Peak calling (histone marks)
- Call peaks with MACS2.
- Calculate and report overlapping peaks from both replicates.
Peak calling (transcription factors)
- Call peaks with SPP.
- Threshold peaks with IDR.
- Report IDR-thresholded peak sets, self-consistency ratio, rescue ratio, reproducibility test.