Fig. 1

Overview of RiboA. a Workflow diagram of using RiboA; b input datasets and parameters for an offset job; c–e results generated from an offset job: c distribution of mRNA fragment size for Frame 0 (blue), Frame 1 (orange) and Frame 2 (green) respectively, d A-site offset table where green indicates that the offset value can be uniquely identified for the fragment size and frame combination while orange indicates that a unique offset cannot be identified and the top two probable offsets are shown in such scenarios, and e distribution of A-site offset among genes; f input datasets and parameters for a profile job; g A-site read density profiles generated from a profile job where each line represents one gene and lists the gene name, number of nucleotides for the gene and read counts for each nucleotide after applying the A-site offset table; h comparison between the raw reads mapped by 5′-end (grey) and the reads after applying the A-site offset value (blue) for the first 30 codons in gene YLR355C. c and e are generated directly from the RiboA web application, and h is plotted in Microsoft Excel by using the data generated from the RiboA web application