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bioRxiv · 10.1101/2020.08.27.267153

Mapping ribonucleotides embedded in genomic DNA to single-nucleotide resolution using Ribose-Map

Gombolay, A.·Storici, F.
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Abstract

Ribose-Map is a user-friendly, standardized bioinformatics toolkit for the comprehensive analysis of ribonucleotide sequencing experiments. It allows researchers to map the locations of ribonucleotides in DNA to single-nucleotide resolution and identify biological signatures of ribonucleotide incorporation. In addition, it can be applied to data generated using any currently available high-throughput ribonucleotide sequencing technique, thus standardizing the analysis of ribonucleotide sequencing experiments and allowing direct comparisons of results. This protocol describes in detail how to use Ribose-Map to analyze raw ribonucleotide sequencing data, including preparing the reads for analysis, locating the genomic coordinates of ribonucleotides, exploring the genome-wide distribution of ribonucleotides, determining the nucleotide sequence context of ribonucleotides, and identifying hotspots of ribonucleotide incorporation. Ribose-Map does not require background knowledge of ribonucleotide sequencing analysis and assumes only basic command-line skills. The protocol requires less than 3 hr of computing time for most datasets and about 30 min of hands-on time.

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Gombolay, A., Storici, F.. 2020-08-27. Mapping ribonucleotides embedded in genomic DNA to single-nucleotide resolution using Ribose-Map. https://doi.org/10.1101/2020.08.27.267153

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