Response to the commentary by Melidis et al. on "Untargeted CUT&Tag reads are enriched at accessible chromatin and restrict identification of potential G4-forming sequences in G4-targeted CUT&Tag experiments"

In their Matters Arising commentary, Melidis et al. critically evaluate our work (Nucleic Acids Research, volume 53, gkaf678). In our response, we emphasize why our approach supports the validity of our conclusions. The authors' suggestion that we failed to include "explicit disclosure of the analytical methods and code" in our original publication is misleading; we used publicly available tools and disclosed explicit parameters and detailed methods for each process in our original publication. While the authors raise several important points, such as the difference in DNA recovery between targeted and untargeted samples, we argue that this difference does not abrogate the need to control for untargeted tagmentation. Due to the co-localization of G4s and preferential Tn5 tagmentation in accessible chromatin, our suggestion that G4 CUT&Tag data be validated is both reasonable and scientifically rigorous.