After I input my bigwig files of my chip-seq and input data, choose the chip-binding targets as the region to be plotted and using reference-point for output, others are default parameter and also default parameter for plotHeatmap (I’m using galaxy).
Turns out that the input have orange lines throughout the heatmap while my ChIP data has a narrow inverted blue triangle at top but bottom are all red, but I expect all genes to have at least a blue region in middle as I already used the chip-binding targets as region to be plotted and I do see a sharp peak at TSS for the curve plot above the heatmap.