Fig. 1

Workflow of NGS-Integrator and example of application in analysis of ChIP-Seq data. a NGS-Integrator pipeline and further applications for integration of multiple genome-wide DNA sequencing data. b Identification of genomic binding sites for transcription factor ELF1 near Eef2 gene. Three replicates of ChIP-Seq data for ELF1 (E74-like factor 1), which is an Ets family TF, were generated in mpkCCD cells. The replicate data tracks were integrated (window size for background noise calculation: 10 kb with 2× median across the window). The NGS-Integrator integrated track (red track) was generated from the three replicates and consensus ELF1 binding motifs (Homer motif database) were indicated by blue lines. ELF1 ChIP-Seq data (ENCSR033OWC) from the mouse ENCODE database with fold change of signal over control track and its optimal irreproducible discovery rate (IDR) threshold peaks (green bars, orange bars indicate summits of peaks) are displayed for comparison. Peaks identified from a conventional peak calling tool MACS2 were labeled by blue bars for peaks from each replicate and purple bar for the conserved peaks across the replicates. In addition, peaks identified using MACS2 (bdgcallpeak, cutoff > 0.5) was also shown below the NGS-Integrator integrated track (red). All data tracks were displayed on the UCSC Genome Browser with mouse genome mm10