GETUTR

GETUTR estimates and quantifies 3' UTR usage from RNA-seq data to annotate 3' UTRs, predict cleavage sites, and detect polyadenylation signals.

Key Features:

• Heuristic and regression methods: Employs heuristic and regression methodologies to estimate and quantify 3' UTR usage directly from RNA-seq data.
• High correlation with experimental data: Produces estimates that correlate highly with 3P-seq experimental results.
• Detection of polyadenylation signals: Identifies polyadenylation signals upstream of predicted cleavage sites to inform mRNA processing analysis.

Scientific Applications:

• Profiling across diverse contexts: Enables comprehensive profiling of 3' UTRs across cell types, developmental stages, and species.
• Functional studies: Facilitates investigation of 3' UTR roles in gene regulation within specific cellular contexts.

Methodology:

Performs preprocessing, smoothing, and normalization of RNA-seq data and applies heuristic and regression methodologies to estimate and quantify 3' UTR usage and detect polyadenylation signals upstream of predicted cleavage sites.