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bioRxiv · 10.1101/694646

Visualizing the periodic Ribo-seq reads with RiboPlotR

Wu, H.-Y. L.·Hsu, P. Y.
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Abstract

BackgroundRibo-seq has revolutionized the study of mRNA translation in a genome-wide scale. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes decipher three nucleotides each time. While the 3-nt periodicity has been widely used to study novel translation events and identify small open reading frames on presumed non-coding RNAs, tools which allow the visualization of those events remain underdeveloped.\n\nFindingsRiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads for all annotated transcript isoforms in a context of a given gene. In particular, RiboPlotR plots Ribo-seq reads mapped in three reading frames using three colors for one isoform model at a time. Moreover, RiboPlotR shows Ribo-seq reads on upstream ORFs, 5 and 3 untranslated regions and introns, which is critical for observing new translation events and potential regulatory mechanisms.\n\nConclusionsRiboPlotR is freely available (https://github.com/hsinyenwu/RiboPlotR) and allows the visualization of the translating features in Ribo-seq data.

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Wu, H.-Y. L., Hsu, P. Y.. 2019-07-08. Visualizing the periodic Ribo-seq reads with RiboPlotR. https://doi.org/10.1101/694646

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