Skip to main content
Fig. 3 | Genome Biology

Fig. 3

From: Identification of transcription factor binding sites using ATAC-seq

Fig. 3

Local nucleosome architecture and footprints. a Cleavage profiles around CTCF ChIP-seq peaks indicate strand-specific cleavage preference left/right of the TF binding site for distinct ATAC-seq protocols in GM12878 cells. Smaller peaks away from the center represent linker regions between histones. b Fragment size distribution for ATAC-seq protocols on GM12878 cells indicates clear peaks representing fragments with particular numbers of nucleosomes. Local minimum values were used to define nucleosome-free fragments Nfr, fragments with one nucleosome 1N and fragments with one or more +2N nucleosomes. c Comparison of HINT-ATAC models with distinct nucleosome decomposition strategies of Omni ATAC-seq (left) and standard ATAC-seq (right) on GM12787 cells. A higher ranking score (y-axis) indicates highest recovery of ChIP-seq supported binding sites. Labels in the x-axis indicate if strand information is used by the model. p values are based on the Friedman-Nemenyi test

Back to article page