The distribution of peak length differed for all model/non-model species pairs.
ChIPseek uses JavaScript in filter criteria (a) Distance to TSS and (b) Peak length to provide slider bars and text boxes for users to specify a range (bp) to filter the peaks according to distance to TSS or peak length.
The toxins with RHS repeats show a peak in their length distribution around 1400 1600 amino acids (second peak in the overall distribution), while for the filamentous hemagglutinin repeats the peak length distribution is 3000 3400 amino acids (the fourth peak in the overall distribution).
The total peak length distribution (i.e. without selective bases) showed that the number of small length peaks greatly exceeded that of longer length peaks for the three genomes.
The default peak length was 1001 bp.
Subsequently, for each species we performed Pearson's correlation between H and the number of peaks per profile, and between H and peak length.
Peak length was the length in nucleotides of the trimmed ChIP-seq peak.
The choice of 200 bp is empirical; we try several values (100 bp, 200 bp, 400 bp, and 800 bp) and consider the one that achieves the best performance, i.e., the highest correlation coefficients (results not shown for other peak lengths).
Allelic ratios were calculated between the two highest peaks with the expected fragment length for heterozygous markers in both tumour and normal DNA.
For the counting statistics, double peaks were detected as an increment of 8 +- 4 nm in contour length for final rupture peaks in the contour length plot, given that the curve showed one of the fingerprints.
