title: RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing.
abstract: The ribosome profiling technique (Ribo-seq) allows the selective sequencing of translated RNA regions. Recently, the analysis of genomic sequences associated to Ribo-seq reads has been widely employed to assess their coding potential. These analyses led to the identification of differentially translated transcripts under different experimental conditions, and/or ribosome pausing on codon motifs. In the context of the ever-growing need for tools analyzing Ribo-seq reads, we have developed 'RiboProfiling', a new Bioconductor open-source package. 'RiboProfiling' provides a full pipeline to cover all key steps for the analysis of ribosome footprints. This pipeline has been implemented in a single R workflow. The package takes an alignment (BAM) file as input and performs ribosome footprint quantification at a transcript level. It also identifies footprint accumulation on particular amino acids or multi amino-acids motifs. Report summary graphs and data quantification are generated automatically. The package facilitates quality assessment and quantification of Ribo-seq experiments. Its implementation in Bioconductor enables the modeling and statistical analysis of its output through the vast choice of packages available in R. This article illustrates how to identify codon-motifs accumulating ribosome footprints, based on data from Escherichia coli.
authors.affiliation: Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Popa
authors.affiliation: Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France.
authors.forename: Kevin
authors.initials: K
authors.lastname: Lebrigand
authors.affiliation: Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France.
authors.forename: Agnes
authors.initials: A
authors.lastname: Paquet
authors.affiliation: Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Nottet
authors.affiliation: Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Robbe-Sermesant
authors.affiliation: Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France.
authors.forename: Rainer
authors.initials: R
authors.lastname: Waldmann
authors.affiliation: Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Barbry
keywords: genomics; ribosome footprints; ribosome profiling