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Semi-automated genome annotation using epigenomic data and Segway

By Eric G. Roberts, Mickaƫl Mendez, Coby Viner, Mehran Karimzadeh, Rachel C. W. Chan, Rachel Ancar, Davide Chicco, Jay R. Hesselberth, Anshul Kundaje, Michael M. Hoffman

Posted 17 Oct 2016
bioRxiv DOI: 10.1101/080382

Biochemical techniques measure many individual properties of chromatin along the genome. These properties include DNA accessibility (measured by DNase-seq) and the presence of individual transcription factors and histone modifications (measured by ChIP-seq). Segway is software that transforms multiple datasets on chromatin properties into a single annotation of the genome that a biologist can more easily interpret. This protocol describes how to use Segway to annotate the genome, starting with reads from a ChIP-seq experiment. It includes pre-processing of data, training the Segway model, annotating the genome, assigning biological meanings to labels, and visualizing the annotation in a genome browser.

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