Fig. 1.

Visualization of pipeline metrics (a) Alignment reproducibility is measured as the correlation between two replicates in the number of reads that fall inside 10 kb genomic bins. Bins with similar read densities in each replicate indicate higher reproducibility; bins with an imbalance signify lower reproducibility. b Open chromatin reproducibility is measured by assessing average peak height across all bases in the window compared between replicates. Collections of bins in which the average peak height is similar between replicates result in high reproducibility scores. c To measure biological significance, known transcription factor binding information from ChIP-seq is compared to predicted protein binding footprints at each site that is a match to a protein’s binding site motif. If the footprint prediction lines up with known ChIP-seq data, the binding motif is a true positive protein binding site; if the footprint prediction does not line up with ChIP-seq data, the binding motif is a false positive. Likewise, if a binding motif lines up with ChIP-seq but has no footprint, it is a false negative, and if the binding motif lines up with neither ChIP-seq nor a footprinting prediction it is a true negative