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RiboDiff: detecting changes of translation efficiency from ribosome footprints

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Item Type:Preprint
Title:RiboDiff: detecting changes of translation efficiency from ribosome footprints
Creators Name:Zhong, Y. and Karaletsos, T. and Drewe, P. and Sreedharan, V. and Kuo, D. and Singh, K. and Wendel, H.G. and Raetsch, G.
Abstract:Motivation: Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case-control studies are needed. Results: We present a statistical framework and analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy. Availability: Source code and documentation are available at http://github.com/ratschlab/ribodiff. Supplementary Material can be found at http://bioweb.me/ribo.
Publisher:Cold Spring Harbor Laboratory Press
Article Number:017111
Date:11 January 2016
Official Publication:https://doi.org/10.1101/017111
Related to:
http://edoc.mdc-berlin.de/16010/Final version

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