Abf1 (A) and Reb1 (B) heat maps of CUT&RUN datasets from a single experiment (20160630), pooling 1” to 32” time-course samples, and separating into ≤120 bp and ≥150 bp size classes (left). Also shown is the ORGANIC ChIP-seq ≤120 bp size class (middle) and standard ChIP-seq datasets (right). Abf1 has two DNA-binding domains spaced ~10 bp apart (Cho et al., 1995), whereas Reb1 has a single Myb-like DNA-binding domain (Morrow et al., 1990). Solubilization of Abf1 chromatin after MNase digestion required 600 mM NaCl to obtain the best trade-off between specificity and sensitivity, whereas for Reb1, 80 mM gave the best results (Kasinathan et al., 2014), and these are the datasets used for comparison. As in our previous comparison of ORGANIC to ChIP-exo and ChIP-chip (Kasinathan et al., 2014), we consider the set of all statistically significant Abf1 and Reb1 motifs as the ‘gold standard’ for judging sensitivity (occupancy of sites by the correct TF) and specificity (exclusion from sites of an incorrect TF). Aligned profiling data were centered and oriented over the motif for the same TF (top) and for the other TF (bottom) for display (removing 81 sites where Abf1 and Reb1 sites were within 50 bp of one another) and were ordered by average pixel density over the −1 kb to +1 kb span of the ≤120 bp datasets using Java Treeview with log2 scaling and contrast = 5. Ordering was performed independently for CUT&RUN (based on ≤120 bp fragments) and ChIP-seq, in which case the approximate fraction of sites occupied relative to flanking regions becomes evident, and comparison of the top panel (correct TF) to the bottom panel (incorrect TF) reflects the sensitivity/specificity tradeoff for a dataset. Sites were determined by MAST searching of the S. cerevisiae genome using the position-specific scoring matrices (PSSMs) based on ChIP-seq data (Figure 1—figure supplement 4), but similar results were obtained using MAST with PSSMs based on CUT&RUN data (not shown).