The Annotate regions task in Flow labels individual peaks as promoters for a particular gene if the peak falls 1000 bases upstream from a gene's transcription start site, or 100 1000 bases downstream from a gene's transcription start site by default. A promoter sum for a given gene is the number of cut sites per cell that fall within all the peaks labeled as promoters (-1000bp ~ 100bp 1000bp by default or user defined through Annotate regions) for that gene. Higher promoter sum values indicate higher chromatin accessibility in the promoter region [1]. 

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