README.md

========== ENCODE ChIP-seq Pipeline

ENCODE Uniform processing pipeline for ChIP-seq

Current implementation is deployed to the DNAnexus platform.

Mapping

1. Map reads with BWA, mark duplicates Picard, and remove duplicates.
2. Estimate library complexity and calculate calculate NRF (non-redundant fraction), PBC1, PBC2 (PCR bottleneck coefficient).
3. Calculate cross-correlation analysis with spp/phantompeakqualtools.
4. Generate p-value and fold-over-control signal tracks for each replicate and replicates pooled with MACS2.

Peak calling (histone marks)

1. Call peaks with MACS2.
2. Calculate and report overlapping peaks from both replicates.

Peak calling (transcription factors)

1. Call peaks with SPP.
2. Threshold peaks with IDR.
3. Report IDR-thresholded peak sets, self-consistency ratio, rescue ratio, reproducibility test.