Fig. 1.

Effect of SICER gap and window parameters in peak calling. (A) Effect of gap size on total island score. The gap size with the highest total score, for a given window size, was chosen as the optimal gap size. (B) Choosing an optimal combination of gap/window size ensured that detected regions were well defined and narrow. The upper panel is a genomic view of Tox and Dam coverage (read density). Below are represented peaks identified with different settings (blue boxes). (C) Overlap of genes identified as Tox targets by different SICER parameters.