title: Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools.
abstract: RNA structure-probing data can improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. In recent years, massive parallel sequencing has dramatically improved the throughput of RNA structure probing experiments, but at the same time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data, we have made a collection of tools, which allow raw sequencing reads to be converted to normalized probing values using different published strategies. In addition, we also provide tools for visualization of the probing data in the UCSC Genome Browser and for converting RNA coordinates to genomic coordinates and vice versa. The collection is implemented as functions in the R statistical environment and as tools in the Galaxy platform, making them easily accessible for the scientific community. We demonstrate the usefulness of the collection by applying it to the analysis of sequencing-based hydroxyl radical probing data and comparing different normalization strategies.
authors.affiliation: Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Lukasz Jan
authors.initials: LJ
authors.lastname: Kielpinski
authors.affiliation: Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Nikolaos
authors.initials: N
authors.lastname: Sidiropoulos
authors.affiliation: Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark. Electronic address: jvinther@bio.ku.dk.
authors.forename: Jeppe
authors.initials: J
authors.lastname: Vinther
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D003196:Computer Graphics; D058893:DNA Barcoding, Taxonomic / Q000379:methods; D015342:DNA Probes / Q000737:chemistry; D057225:Data Mining; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data*; D017665:Hydroxyl Radical / Q000737:chemistry; D015233:Models, Statistical; D015335:Molecular Probes / Q000737:chemistry; D008969:Molecular Sequence Data; D012313:RNA / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data*; D012984:Software
chemical_list: D015342:DNA Probes; D015335:Molecular Probes; D017665:Hydroxyl Radical; D012313:RNA
keywords: Bioconductor; Galaxy; Normalization; Probing; RNA; Sequencing; Structure; Winsorization