Fig 1. Overview of the CoRE-ATAC framework.

Paired-end ATAC-seq data captures different cut and insert size distributions corresponding to the presence or absence of nucleosomes or TFs. ATAC-seq data is encoded into a 10x600 matrix and 19 data features from PEAS algorithm to predict the functionality of an open chromatin region, using both novel and manually selected features. In the final step, CoRE-ATAC classifies cis-REs into 4 functional classes: promoter, enhancer, insulator, and other.