Semi-automated genome annotation using epigenomic data and Segway
Eric G. Roberts,
Rachel C.W. Chan,
Jay R. Hesselberth,
Michael M. Hoffman
Posted 17 Oct 2016
bioRxiv DOI: 10.1101/080382
Posted 17 Oct 2016
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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