Chunk #52 — Online Methods — 1. Data matrix, primary analysis and processing, quality control — 1.2 ChIP-seq and DNase-seq uniform reprocessing for consolidated epigenomes — c. Peak Calling
For the histone ChIP-seq data, the MACSv2.0.10 peak caller was used to compare ChIP-seq signal to a corresponding whole cell extract (WCE) sequenced control to identify narrow regions of enrichment (peaks) that pass a Poisson p-value threshold 0.01, broad domains that pass a broad-peak Poisson p-value of 0.1 and gapped peaks which are broad domains (p < 0.1) that include at least one narrow peak (p < 0.01) (https://github.com/taoliu/MACS/)32. Fragment lengths for each dataset were pre-estimated using strand cross-correlation analysis and the SPP peak caller package (https://code.google.com/p/phantompeakqualtools/)37 and these fragment length estimates were explicitly used as parameters in the MACS2 program (--shift-size=fragment_length/2).
