RT Journal Article SR Electronic T1 Semi-automated genome annotation using epigenomic data and Segway JF bioRxiv FD Cold Spring Harbor Laboratory SP 080382 DO 10.1101/080382 A1 Eric G. Roberts A1 Mickaƫl Mendez A1 Coby Viner A1 Mehran Karimzadeh A1 Rachel Chan A1 Rachel Ancar A1 Davide Chicco A1 Jay R. Hesselberth A1 Anshul Kundaje A1 Michael M. Hoffman YR 2016 UL http://biorxiv.org/content/early/2016/10/17/080382.abstract 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.