Comparison with MACS and FindPeaks
We compared HATSEQ with two state-of-the-art methods and here we provide some additional information whether detected regions may have been "sliced". Meaning that, instead of the detection of a single region, two very close neighboring regions are detected.
HATSEQ detects 14,616 ROIs regions in the H3K4me data set. Using the same data set, MACS detected 10,694 and FindPeaks: 9,471 ROIs.
In the underneath table we illustrate the distances between neighboring regions for each of the method.
HATSEQ detects 6 ROIs that are located within a distance of 100nt from a neighboring ROI. MACS finds 9 ROIs and FindPeaks 41 ROIs that are located within a distance of 100nt from a neighboring ROI.
For a distance of 1000nt between two adjacent ROI, we find 1924 ROIs for HATSEQ. However, 1316 ROIs were overlapping with the ROI detected by either Findpeaks or MACS. Only 608 ROIs (0.46%) showed to be solely detected by HATSEQ and were neighboring a ROI within 1000nt. An additional test showed that the large majority of these regions showed the expected bimodal distribution.