Computational analysis demonstrates two graphical criteria for V-plots, indicating reliable transcription factor footprint discovery across chromatin accessibility sequencing datasets.
A recent study reported sequence biases in transcription factor (TF) footprinting data, and expressed concern about the accuracy in TF footprint discovery using V-plot analysis. Here we define two graphical parameters of V-plot as important criteria to implement into future analysis. Guaranteed by the criteria, V-plot still serves as a powerful and straightforward tool for TF footprint discovery from various chromatin accessibility sequencing datasets.
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Zhang et al. (2026) studied this question.
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