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README.md

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-chip-seq-pipeline
+==========
+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.