Fig. 4

Application of the CUT&RUN suspect lists on published datasets. A Principal component analysis on published C&R datasets (top row) and Scree plots (bottom row) from [11], showing that suspect list filtering reduces sample similarity and allows samples to clustering as expected based on the antibody used. This was confirmed by calculation of the average ratio of inter-target versus intra-target distance, which increased with filtering from 2.68:1 to 4.73:1 in HEK293T and from 2.18:1 to 8.53:1 in the mouse hindlimb. B Evaluation of suspect list filtering on SEACR peak calling. Left: Comparison of peaks called using SEACR against a negative control on relaxed and stringent modes for the β-catenin A replicate, showing that suspect list filtering of BAM files before peak calling leads to a smaller number of called peaks which have an increased average signal profile within the peaks and an increased percentage of peaks which contain expected TCF/LEF motifs (middle). The increase in background signal in the filtered and more stringent sets in the average profile (left) is due to an increase in peaks called in high-signal regions, not suspect list filtering (see Supplementary Fig. 1D). Right: Comparison of peaks called by SEACR on MYC and MAX datasets from [1] before and after suspect list filtering, showing a decrease in peak number accompanied by an increase in average signal within the peak regions. C Evaluation of suspect list filtering on MACS2 peak calling. Left: calling β-catenin peaks with MACS2 after filtering leads to peaks with a comparable but slightly higher average signal profile. Center: Peak calling with MACS2 on MYC and MAX at two different stringencies before and after filtering shows that suspect list regions are called as peaks in unfiltered sets and that filtered sets contain more peaks at the same statistical stringency. Right: The average profiles of filtered MYC and MAX peak sets show a higher signal to noise ratio than their unfiltered counterparts. C&R, CUT&RUN; PCA, principal component analysis