Additional file 4: of ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference

Figure S3. Visual inspection reveals consistent overlap between HOMER peaks and OCRs at peak size of 200. (a) Read coverage for DNase1-seq (top) and ATAC-seq (bottom) shown underneath open chromatin regions called by HOMER at peak sizes ranging from 10 base pairs to 2000 base pairs. Peak reproducibility between replicates was shown to be higher with lower peak sizes. Visualized using the Broad Institute’s Integrative Genomics Viewer (software. broadinstitute.org/software/igv /). (b,c,d) Metrics of reproducibility and biological information plotted against the HOMER argument minDist for all pipelines. Pipelines could have a minDist of 0, 50 or 500, and these values had no effect on correlation between replicates or recapitulation of known ChIP-seq. (PDF 1272 kb