riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data
Fig 3
(A) Percentage of P-sites in the three frames (Periodicity score) along the 5’ UTR, CDS and 3’ UTR from ribosome profiling performed in mouse brain (GSE102318). The statistical significances from two-tailed Wilcoxon–Mann–Whitney test comparing RiboProfiling and Plastid with respect to riboWaltz are reported (P-value: ** < 0.01, *** < 0.001). (B) Meta-profiles showing the periodicity of ribosomes along the transcripts at the genome-wide scale. The three metaprofiles are based on the P-site identification obtained by using riboWaltz, RiboProfiling and Plastid. The shaded areas to the left of the start codon highlight the shift of the periodicity toward the 5’ UTR that is absent in the case of data analysed using riboWaltz. (C) Comparison between the codon usage index based on in-frame P-sites from riboWaltz and RiboProfiling (left panel) and between the codon usage index based on in-frame P-sites from riboWaltz and Plastid (right panel). The length of the reads ranges from 19 up to 38 nucleotides (see Table 1) with the optimal PO used in the correction step of riboWaltz being 16 nucleotides from the 3’ end.