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 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 ~ 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].
Flow task Promoter sum matrix summarizes each promoter sum and outputs a cell x gene matrix. In the matrix, only genes that have peaks within its promoter region have been included. In Flow Promoter sum matrix can be invoked in the Peak analysis section by clicking the Annotated regions data node (Figure 1).
To run Promoter sum matrix in Flow,
Click the Annotated regions data node
Click the Peak analysis section in the toolbox
Click Promoter sum matrix
Once the task has been finished, a new data node will be produced where the promoter sum value for each feature can be used to color UMAP/T-SNE and to determine cell type (Figure 2).
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