Fig. 5

A partial set of outputs of the full pipeline and component workflows. See Fig. 6 for more outputs. All of these are outputs of all the full workflows, except some are not available in the pipeline beginning with only peak data. Each individual output is available as the product of individual workflows or as standalone R scripts (see Table 2). All data is from analysis of the H3K4me3 dataset except E, which is from analysis of the GATA1 dataset. a GeneratePeakExamples component output. (left) A predicted peak (x-axis: chr11:113174680–113196653) (right) A non-peak region (x-axis: chr3:50344686–50349686). Also see Fig. 3. b Partial output of CalcPeakStats module. c Partial output of mapping to genes workflow (AnnotatePeaks). Several additional columns of information are not shown here and full table has many more rows. d (i) Heatmap of coverage around transcription start sites (TSSs). (ii) Density plot of coverage around TSSs. (iii) Table of distances from TSS. Note expected pattern of TSS-centric location of H3K4me3, as indicated in previous studies. e Output of motif discovery component for GATA1 dataset. Note close match to expected GATA1 motif [27] is obtained, including central GATA motif (positions 2–5). f Comparison of workflow-generated UCSC track (top) to ENCODE-generated UCSC track (middle) for H3K4me3 dataset. Image from UCSC browser