PT  - JOURNAL ARTICLE
AU  - Ferhat Alkan
AU  - Joana Silva
AU  - Eric Pintó Barberà
AU  - William J. Faller
TI  - <em>Ribo-ODDR</em>: Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs
AID  - 10.1101/2020.01.12.900175
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.01.12.900175
4099  - http://biorxiv.org/content/early/2020/01/14/2020.01.12.900175.short
4100  - http://biorxiv.org/content/early/2020/01/14/2020.01.12.900175.full
AB  - Ribosome profiling (Ribo-seq) has revolutionized the study of RNA translation. The technique provides information on ribosome positions across all translated RNAs with nucleotide-resolution. However, several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of ribosomal RNA (rRNA) fragments. Various strategies have been employed to tackle this issue, including the use of commercial rRNA depletion kits, however these may perform suboptimally. Here we show that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a “one-size-fits-all” approach may result in inefficient rRNA depletion. In order to overcome this it is possible to use custom-designed biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oli-gos. We have developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oli-gos. We show that Ribo-ODDR designed oligos lead to a significant increase in rRNA depletion, and increased sequencing depth as a result. Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR