SPLICE-q

SPLICE-q quantifies splicing efficiency genome-wide from aligned RNA-seq reads to measure intron excision and post-transcriptional transcript processing.

Key Features:

• Genome-Wide Quantification: Evaluates splicing efficiency of individual introns across the entire genome.
• Strand-Specific RNA-seq Support: Leverages aligned reads from strand-specific RNA-seq data to improve sensitivity and accuracy of splicing measurements.
• Customizable Overlap Sensitivity: Allows adjustable restrictiveness for intron overlap with other genomic elements such as exons from different genes.

Scientific Applications:

• Transcript Processing Dynamics: Used to study the implications of splicing efficiency in transcript processing dynamics.
• Disease Research: Aids investigation of perturbations from aberrant transcript processing that are linked to human diseases.
• Cancer Progression Studies: Applied to intron excision dynamics in yeast and human nascent RNA-seq and to total RNA-seq from patient-matched prostate cancer samples to provide insights beyond gene expression levels.

Methodology:

SPLICE-q analyzes aligned RNA-seq reads to compute splicing efficiency for each intron individually and supports adjustable restrictiveness for intronic overlap with other genomic elements.