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bioRxiv · 10.1101/169862

riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data

Lauria, F.·Tebaldi, T.·Bernabo, P.·Groen, E. J. N.·Gillingwater, T. H.·Viero, G.
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Abstract

Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies.\n\nAvailability and ImplementationriboWaltz was implemented in R and is available at https://github.com/LabTranslationalArchitectomics/RiboWaltz\n\nContactgabriella.viero@cnr.it or fabio.lauria@unitn.it

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Lauria, F., Tebaldi, T., Bernabo, P., Groen, E. J. N., Gillingwater, T. H., Viero, G.. 2017-07-28. riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data. https://doi.org/10.1101/169862

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