Fig. 2
From: NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data
Aggregate profiles showing nucleosome density around the centres of LOCK regions (large organized chromatin K9me2 modifications) in ESCs [96]. a Calculation using NucTools (grey) and the corresponding Savitzky-Golay smoothing of this curve (red). A clear increase of nucleosome density is seen as a characteristic of LOCKs. b Calculation using HOMER in its default mode. Large peaks resulting from sequencing artefacts seen on the left from the centre preclude proper identification of the shape of the aggregate profile. HOMER’s advanced mode -histNorm allows suppressing these artefacts making the curve more similar to the curve in panel (a) (data not shown). The accumulation of sequencing artefacts strongly interfering with large-scale analysis of aggregate profiles is a standard problem