Clirc

Clirc identifies RNA-binding protein (RBP)-bound circular RNAs (circRNAs) from CLIP-Seq and RNA-Seq data to profile RBP-circRNA interactions and study circRNA biogenesis and function.

Key Features:

• RBP-circRNA Interaction Profiling: Analyzes CLIP-Seq datasets to detect circRNAs bound by RBPs and profile their interactions.
• Compatibility with CLIP-Seq Variants: Supports HITS-CLIP, PAR-CLIP, and iCLIP experimental variants.
• Alignment Capabilities: Employs the gsnap aligner for alignment of CLIP-Seq reads, addressing typically short read lengths.
• User-Supplied Coordinates: Accepts known circRNA coordinates from previous studies or RNA-Seq analyses to refine identification.
• General RNA-Seq Data Compatibility: Can process general RNA-Seq data with a preference for non-polyA selected datasets.

Scientific Applications:

• Genome-wide RBP-circRNA Profiling: Enables genome-wide identification of RBP-bound circRNAs from CLIP-Seq datasets.
• CircRNA Biogenesis and Function Studies: Facilitates investigation into circRNA formation and functional roles via RBP interaction data.
• Regulatory Role Characterization: Supports studies of circRNA–RBP regulatory effects on gene expression and cellular processes.

Methodology:

Repurposes existing CLIP-Seq datasets, aligns reads with gsnap, and integrates user-supplied circRNA coordinates to detect RBP-bound circRNAs while accommodating short CLIP-Seq read lengths.