PT - JOURNAL ARTICLE AU - Eric G. Roberts AU - Mickaƫl Mendez AU - Coby Viner AU - Mehran Karimzadeh AU - Rachel Chan AU - Rachel Ancar AU - Davide Chicco AU - Jay R. Hesselberth AU - Anshul Kundaje AU - Michael M. Hoffman TI - Semi-automated genome annotation using epigenomic data and Segway AID - 10.1101/080382 DP - 2016 Jan 01 TA - bioRxiv PG - 080382 4099 - http://biorxiv.org/content/early/2016/10/17/080382.short 4100 - http://biorxiv.org/content/early/2016/10/17/080382.full AB - 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.