Fig. 4

Evaluation: Binding characteristics. a, b 5’ end coverage around motif centered predicted binding sites for two biological replicates of Dorsal. The two peaks on the forward and reverse strand have a distance of 18 bp, which is in line with a previous analysis [11] of the same data. c, d Using standardized parameter settings for all samples, no characteristic distribution is derived for TBP. See Additional file 1: Figure S4 for further positive and negative examples. e, f Difference of qfrag-length distribution between original datasets and pseudo-controls for Dorsal replicates (for all mapped reads (blue) and filtered for reads that map to standard chromosomes (green)). The estimated protected-region width of ℓ ^′′′=18 is consistent with the distance derived by the 5’ end coverage around motif centered binding sites. The signatures are independent of whether mapped reads were filtered or not. Furthermore, they are reproducible for biological replicates. g, h Additional examples for biological replicates of TBP. The signatures are reproducible for biological replicates, but different from the signatures derived for Dorsal. See Additional file 1: Figure S6 for further examples