RT Journal Article SR Electronic T1 RiboDiff: Detecting Changes of mRNA Translation Efficiency from Ribosome Footprints JF bioRxiv FD Cold Spring Harbor Laboratory SP 017111 DO 10.1101/017111 A1 Yi Zhong A1 Theofanis Karaletsos A1 Philipp Drewe A1 Vipin Sreedharan A1 David Kuo A1 Kamini Singh A1 Hans-Guido Wendel A1 Gunnar Rätsch YR 2016 UL http://biorxiv.org/content/early/2016/01/11/017111.abstract AB 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 RiboDiff webpage http://bioweb.me/ribodiff. Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff.Contact zhongy{at}cbio.mskcc.org and Gunnar.Ratsch{at}ratschlab.org.