CLASH Analyst

CLASH Analyst analyzes raw CLASH (crosslinking, ligation, and sequencing of hybrids) data to identify and annotate in vivo RNA-RNA interactions, including chimeric reads that link regulatory RNAs such as miRNAs and piRNAs to their target molecules.

Key Features:

• Raw CLASH data input: accepts raw CLASH sequencing data for direct analysis.
• Identification of RNA chimeras: detects chimeric reads comprising regulatory RNAs (miRNAs, piRNAs) and their target molecules.
• Detailed annotation: annotates identified RNA-RNA interactions with transcript-level information.
• Transcriptome-wide interaction mapping: maps RNA-RNA interactions across the transcriptome from CLASH datasets.
• Reanalysis of published datasets: enables reanalysis of previously published CLASH data to uncover additional interactions.

Scientific Applications:

• Gene regulation studies: mapping RNA-RNA interactions to investigate regulatory roles of non-coding RNAs such as miRNAs and piRNAs.
• Transcriptome-wide interaction mapping: enabling comprehensive studies of interaction networks across the transcriptome.
• Validation and extension of published CLASH data: confirming and expanding findings from existing CLASH datasets.

Methodology:

Identifies chimeric reads from CLASH data, processes those reads to extract RNA-RNA interaction pairs, and annotates the resulting interactions.