Fig. 2

RiboStreamR Data Processing Pipeline. a Overview of flow of data from sample collection within a lab to processing in R. The red boxes and arrows are steps which are not handled by riboStreamR, while those in blue are handled within riboStreamR. b RiboStreamR requires input of three file types: a set of Bam files, a genome annotation file, and a fasta file containing the genome nucleotide sequences. c The uploaded sequencing data are converted into a GRanges object, where each row is an individual alignment, and every column contains attribute information (metadata) about the alignment. d P-site adjustment method. Reads are separated by length and a meta-gene read density plot around the translation start sites is produced for each read length. The p-site adjustment for each respective alignment length is chosen to be the distance from the largest in-frame upstream peak to the translation start site