PT  - JOURNAL ARTICLE
AU  - Fabio Lauria
AU  - Toma Tebaldi
AU  - Paola Bernabò
AU  - Ewout J.N. Groen
AU  - Thomas H. Gillingwater
AU  - Gabriella Viero
TI  - riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data
AID  - 10.1101/169862
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 169862
4099  - http://biorxiv.org/content/early/2017/07/28/169862.short
4100  - http://biorxiv.org/content/early/2017/07/28/169862.full
AB  - 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.Availability and Implementation riboWaltz was implemented in R and is available at https://github.com/LabTranslationalArchitectomics/RiboWaltzContact gabriella.viero{at}cnr.it or fabio.lauria{at}unitn.it