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The Quantify regions dialog includes configuration options for generating the union set of unique regions and quantify quantifying reads to the regions (Figure 1). 

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Quantify regions generates a counts data node with the number of counts of in each region for each sample. This data node can be annotated with gene information using the Annotate regions task and analyzed using tasks that take counts data as input, such as normalization, PCA, and ANOVA. For ChIP-Seq experiments with input control samples, the Normalize to baseline task can  task can be used prior to downstream analysis.

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