BINDdetect vs plotHeatmap

[mbergsland]

Hi First of all, thanks a lot for such a nice and useful tool!

I have two sets of ATAC-samples; control cells and cells over-expressing TF A. I have ChIP-seq peaks for TF A which are the regions that I have investigated for footprints with TOBIAS. Importantly, centrally enriched TF Motif analysis of ChIP-seq peaks showed centrally enriched motif of TF A, but also a very strong centrally enriched motif of non-related TF B. With this background, my main question to solve with TOBIAS was whether TF A and TF B bind together or exclusive of each other (TF A is not expressed in control condition). From BINDdetect, volcano plot shows TF A footprints and TF B footprints on each side which would, I guess, suggest that the 2 factors do not bind together but rather exclusive of each other (fig1). Considering the strong centrally enriched motifs of both factors within the examined peaks, I assume that the majority of the signals come from the center of these peaks Higher score is shown for TF A in control sample (sample 204) and for TF B in sample with overexpression of TF A (sample 201) in the volcano plot (fig1). This does not make sense since TF A is overexpressed in sample 201 and should show stronger footprints than control sample 204 (binding of TF A is also confirmed from ChIP-seq). Moreover, in the plots from plotHeatmap, footprints (fig2) from TF A is seen in sample 201 and not in sample 204. For TF B the footprint seem stronger for 201. These results seem to be opposite to what is seen in the volcano plot (TF A and TF B footprints increased in each sample, not the same), why is that? It would be very helpful to understand these data properly. I also have a question regarding plotAggregate. Fig3 shows one single region with all footprint signals (bed file with one region), is zero referring to the middle of the peak in this case? What is zero referring to when several regions are analyzed by this function?