Ribotools#
Introduction#
Ribotools is a toolbox for the analysis of matched ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq) data. It uses Rp-Bp for periodicity estimation, and follows the same alignment workflow, directory structure, and naming convention.
Ribotools can be used in combination with Rp-Bp, or directly from raw reads, to generate count tables for Ribo-seq, RNA-seq, or both. It uses HTSeq for abundance estimation.
Ribotools include scripts to calculate translation efficiency (TE) and differential expression (DE). Translation efficiency can be defined as the number of ribosomes per feature, typically a gene, normalized to abundance. A feature can be regulated transcriptionally and/or translationally, resulting in several different regulatory profiles. Differential expression is based on Ribo-seq periodic fragment lengths and can be used to find regulated Ribo-seq ORFs across conditions. Both approaches use DESeq2 to accommodate for sample-to-sample variance, complex experimental designs, and/or confounding factors.