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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 B. 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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