Examples of ggRibo and ggRibo_tx plots for the human MRPL11 gene. Different display options using ggRibo to present RNA-seq and Ribo-seq profiles of the human nuclear-encoded MRPL11 gene. The human embryonic stem cell (ESC) Ribo-seq and RNA-seq data are from Chothani et al. (2022). RNA-seq coverage is shown with a light-yellow background. Ribo-seq reads are presented with their first nucleotide of the P-site, and they are color-coded in red, blue, and green to indicate they map to reading frames 0 (expected), 1, and 2, respectively. MRPL11 possesses five annotated transcript isoforms, and both a uORF and the main ORF are translated. The user can specify which transcript isoform to focus on and can assign the reading frame according to its gene structure; here, ENST00000310999 is selected (bolded). Within the gene models, black boxes indicate the coding sequence (CDS) (i.e., the annotated/main ORF); yellow box(es) indicate the uORF region; and gray and white boxes indicate 5′ UTR and 3′ UTR, respectively. Black and gray vertical dashed lines represent the start and stop codons, respectively, for the annotated mORF. Orange solid and dashed vertical lines represent start and stop codons, respectively, for the uORF. Reads outside of the ORF range are shown in gray. Genomic or transcript coordinates on the chromosomes are indicated below the gene models. (A) Only Ribo-seq and RNA-seq profiles are presented on top of the annotated gene models. (B) An additional DNA sequence track was added, but only the start and stop codons are displayed owing to the large span (>201 nt). (C) The view is further zoomed in on the uORF region, showing both the DNA nucleotide and amino acid sequence tracks in detail (when length <201 nt). Note that the line width of the Ribo-seq reads could be modified by the “ribo_linewidth” parameter, and the sequence color may be modified by the “nucleotide_color_scheme” parameter. (D) Single-transcript plot by ggRibo_tx to show the RNA-seq and Ribo-seq reads that map to the main expressed isoform ENST00000310999. (E) Similar to D, but for a very lowly expressed isoform ENST00000329819 in this data set (see A). The arrow highlights exon 5, which contains a small number of Ribo-seq reads with 3 nt periodicity.