RNAprobR

RNAprobR analyzes RNA structure-probing Next Generation Sequencing (NGS) data to convert raw sequencing reads into normalized probing values, enable coordinate conversion between RNA and genomic coordinates, support visualization in the UCSC Genome Browser, and export results in table and UCSC-compatible bedgraph formats for study of RNA secondary and tertiary structures.

Key Features:

• Normalization Strategies: Functions convert raw sequencing reads into normalized probing values and support various published normalization strategies.
• Data Visualization: Outputs are prepared for visualization in the UCSC Genome Browser to inspect structural signals along sequences.
• Coordinate Conversion: Utilities convert coordinates between RNA and genomic coordinate systems to integrate RNA structure data with genomic context.
• Data Export Options: Analysis results can be exported in table formats and as UCSC-compatible bedgraph files for downstream analysis.

Scientific Applications:

• RNA secondary structure analysis: Enables investigation and interpretation of RNA secondary structure from structure-probing NGS data.
• RNA tertiary structure inference: Supports analysis that aids prediction and interpretation of tertiary structural features.
• Condition-dependent structural changes: Facilitates identification of structural changes occurring under different biological conditions or in response to stimuli.
• Functional implication studies: Assists in relating RNA structural dynamics to potential functional consequences in cellular processes.

Methodology:

Converts raw sequencing reads to normalized probing values using published normalization strategies; generates outputs for UCSC Genome Browser visualization; performs coordinate conversion between RNA and genomic coordinates; exports results as tables and UCSC-compatible bedgraph files; implemented as an R package and as tools on the Galaxy platform.