Chromatin organization and epigenetic marks play a critical role in stem cell pluripotency and differentiation. Chromatin digestion by micrococcal nuclease (MNase) followed by high-throughput sequencing (MNase-seq) is the most widely used genome-wide method for studying nucleosome organization, that is, the first level of DNA packaging into chromatin. Combined with chromatin immunoprecipitation (ChIP), MNase-ChIP-seq represents a high-resolution method for investigating both chromatin organization and the distribution of epigenetic marks and histone variants. The plot2DO package presented here is a flexible tool for evaluating the quality of MNase-seq and MNase-ChIP-seq data, and for visualizing the distribution of nucleosomes near the functional regions of the genome. The plot2DO package is open-source software, and it is freely available from https://github.com/rchereji/plot2DO under the MIT license.
CITATION STYLE
Beati, P., & Chereji, R. V. (2020). Creating 2D occupancy plots using plot2DO. In Methods in Molecular Biology (Vol. 2117, pp. 93–108). Humana Press Inc. https://doi.org/10.1007/978-1-0716-0301-7_5
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