Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq

Accurate detection of transcription factor and nucleosome occupancy from ATAC-seq is challenging due to sequence-dependent Tn5 cleavage bias. TraceBind performs sample-specific Tn5 bias correction by fine-tuning a pretrained cleavage model using mitochondrial DNA reads, followed by multiscale footprint detection with empirical false discovery rate control.