Semi-automated genome annotation using epigenomic data and Segway

Roberts, E. G.; Mendez, M.; Viner, C.; Karimzadeh, M.; Chan, R. C. W.; Ancar, R.; Chicco, D.; Hesselberth, J. R.; Kundaje, A.; Hoffman, M. M.

doi:10.1101/080382

bioRxiv · 10.1101/080382

Semi-automated genome annotation using epigenomic data and Segway

Roberts, E. G.·Mendez, M.·Viner, C.·Karimzadeh, M.·Chan, R. C. W.·Ancar, R.·Chicco, D.·Hesselberth, J. R.·Kundaje, A.·Hoffman, M. M.

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Abstract

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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Roberts, E. G., Mendez, M., Viner, C., Karimzadeh, M., Chan, R. C. W., Ancar, R., Chicco, D., Hesselberth, J. R., Kundaje, A., Hoffman, M. M.. 2016-10-17. Semi-automated genome annotation using epigenomic data and Segway. https://doi.org/10.1101/080382

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