ATAC-seq profiles around transcription factor binding sites

To plot ATAC-seq profiles around transcription factor binding sites (TFBSs), we conducted footprinting with HINT from the RGT library (v0.13.1) (Li et al. 2019). An ATAC-seq model and paired-end data were specified for tool execution, using aligned read BAM files and ATAC-seq peaks in BED format. Once footprints were called, overlapping TFBSs were found using the RGT-matching motif tool and the complete JASPAR motifs database. For REST (MA0138.2), we selected only footprints overlapping a REST ChIP-seq peak using ChIPpeakAnno (v3.18.1), GenomicRanges (v1.36.0), and Bioconductor (v3.9.0) R (v3.6.3) and lifting to mm10. Normalized ATAC-seq profiles around TFBSs of interest were generated with HINT for a 500-bp window size, enabling ATAC-seq bias correction.