Addressing technical variations in ATAC-seq data and improving motif accessibility analyses

Tagmentation-based methods such as ATAC-seq and Cut&Tag have provided easy ways to profile the epigenome in low-input samples and even single cells. In this contribution, we discuss forms of bias (i.e. technical variations) in tagmentation-based data, in particular ATAC-seq, and introduce three R/bioconductor packages to facilitate bulk and single-cell epigenomic data analysis, with a special focus on motif accessibility analysis. The weightedMotifAccess package uses weight models to enable motif accessibility analysis, including transcription factor footprint information. The betterChromVAR package provides a novel, analytical re-implementation of the popular chromVAR method that offers substantial speed improvements, eliminates stochasticity, and offers additional features. Based on this, we also propose a method, CVnorm, that outperforms alternatives in normalizing technical bias in peak count data. The computational efficiency of these tools further enables a new framework for systematically investigating synergistic and antagonistic interactions between transcription factor motifs. Finally, the epiwraps package streamlines the visualization, normalization, and summarization of epigenomic data.