Figure 4

MACS model for ChIP-Seq tags of NAC and YABBY transcription factor using ChIP-Seq data. The red curve represents ChIP-Seq reads on the positive strand and the blue curve represents reads on the negative strand. The black curve illustrates the distribution of reads after shifting them towards 3′-end to get most likely protein-DNA interactions. (a) MACS software builds model for NAC transcription factor using the bimodal distribution of forward (+) and reverse (−) sequence tags. It calculates the estimated DNA fragment size, d =110 which is the distance between the peak in the forward and reverse strand. Then MACS shifts all the tags by d/2 = 55 bp towards the 3′ ends. (b) Similarly MACS builds peak model for YABBY transcription factor. The estimated DNA fragment size, d =104 and MACS shifts all the tags by d/2 = 52 bp towards the 3′ ends to get most likely TF-DNA interactions.