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Intersecting peak lists is the most conservative approach, and retains a small number of high quality peaks.
Mean coverage at common peaks was almost always higher than at sample specific peaks, confirming that intersecting peak lists indeed selects peaks of higher signal to noise ratio.
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Using intersection strategy can filter the false positive peaks, however intersecting too many peak calling tools may let the unfit tool filter out the good peaks.
For the method without mode signs, one can notice the existence of "mirror solutions" which is a line of secondary peaks intersecting with the primary peaks line indicating the true source positions.
Any regions found in both MACS and BayesPeak in human, but that did not intersect any peak in chimpanzee or rhesus macaque, were isolated.
A cutoff of RPKM > 1 was set, and only miRNAs, smaller than 200 bp, intersecting these RNAPII peak regions were considered.
In addition to more and broader peaks in the HM datasets, we observed that the HM datasets also tend to have a higher proportion of peaks intersecting two or more gene loci compared with TF datasets.
The intersection analyses showed that in all FUS peak categories, most peaks intersected with RNAPII binding (Fig. 5b).
Cross-section intersecting the gradient's peak: f 5, y ).
Mapped ChIP tags were analyzed by intersecting MACS and Grizzly Peak algorithms (Zhang et al., 2008; Feng et al., 2011; Harrison et al., 2011) to identify binding regions for each factor.
We next examined whether FUS and EWS ChIP-seq peaks were intersecting (defined as an overlap of at least one base pair) with RNAPII ChIP-seq peaks.
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