RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

• DOI: 10.1093/bioinformatics/btw585
• Publication Date: 2016-09-16T00:10:35Z
• Authors: Yi Zhong; Theofanis Karaletsos; Philipp Drewe; Vipin T Sreedharan; David Kuo; Kamini Singh; Hans-Guido Wendel; Gunnar Rätsch
• Keywords: Ribosome profiling

Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, observed profile is fundamentally confounded by transcriptional activity. In order to decipher principles translation regulation, tools that reliably detect changes in efficiency case-control studies are needed.We present a statistical framework and an analysis tool, RiboDiff, genes with across experimental treatments. RiboDiff uses generalized linear models estimate over-dispersion RNA-Seq measurements separately, performs test for differential using both mRNA abundance occupancy.RiboDiff webpage http://bioweb.me/ribodiff Source code including scripts preprocessing FASTQ data available at http://github.com/ratschlab/ribodiff CONTACTS: [e-mail] or [e-mail] information: Supplementary Bioinformatics online.