Ribotools¶
Introduction¶
Ribotools is a toolbox for the analysis of matched ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq) data. Ribotools can be used in combination with Rp-Bp, or as a standalone software to generate count tables from raw Ribo-seq reads, raw RNA-seq reads, or both, and to calculate translation efficiency (TE) and differential expression (DE).
Ribotools uses Rp-Bp for periodicity estimation, and follows the same alignment workflow, directory structure, and naming convention. It uses HTSeq for abundance estimation.
Ribotools can find TE and/or DE regulated Ribo-seq ORFs across conditions, using Ribo-seq periodic fragment lengths only. Both approaches use DESeq2 to accommodate for sample-to-sample variance and/or confounding factors.