YODEL

YODEL calls peaks from HITS-CLIP (CLIP-SEQ) sequencing data to identify RNA–protein interaction sites such as Argonaute–microRNA–mRNA binding locations.

Key Features:

• Heuristic Peak Calling Approach: Iteratively identifies the tallest point within clustered HITS-CLIP reads and examines bases upstream and downstream to define peak boundaries, avoiding fixed-interval binning used by tools such as Piranha.
• Visualization of Read Peaks: Produces visual representations of read clusters that map to the same genomic region to aid identification of interaction sites.
• Per-Sample Peak Counts: Outputs per-sample peak counts to support downstream quantitative analyses including differential representation studies.

Scientific Applications:

• RNA–protein interaction mapping: Identification of genome-wide interaction sites between proteins and RNAs, including Argonaute-associated sites.
• microRNA binding site discovery: Precise definition of microRNA binding sites and their mRNA targets to inform studies of gene regulation.
• Comparative analysis: Use of per-sample peak counts to compare peak representation across samples or conditions.

Methodology:

YODEL maps HITS-CLIP reads to the genome and applies a heuristic algorithm that iteratively finds the tallest point within clustered reads and examines upstream and downstream bases to define peak boundaries without binning by read start; it generates per-sample peak counts.