AtacWorks: A deep convolutional neural network toolkit for epigenomics

We introduce AtacWorks (https://github.com/clara-genomics/AtacWorks), a method to denoise and identify accessible chromatin regions from low-coverage or low-quality ATAC-seq data. AtacWorks uses a deep neural network to learn a mapping between noisy ATAC-seq data and corresponding higher-coverage or higher-quality data. We apply this approach to as few as 50 hematopoietic stem cells to identify regulatory elements that are differentially-accessible between rare lineage-primed cell subpopulations. dscATAC-seq of FACS-isolated hematopoietic stem cells