SplicePlot

SplicePlot visualizes alternative splicing events and splicing quantitative trait loci (sQTL) effects at the population level using RNA sequencing and genotype data.

Key Features:

• Input Compatibility: Accepts mapped RNA sequencing reads in BAM format and genotype data in VCF format.
• Visualization Outputs: Produces Sashimi plots, hive plots, and structure plots to represent splicing events and genotype-dependent splicing patterns, suitable for publication-quality figures.
• Implementation: Implemented in Python.
• Platform Support: Runs on Linux and Mac OS.

Scientific Applications:

• sQTL analysis: Visualizes the effects of splicing quantitative trait loci on transcript structure across populations.
• Mechanistic splicing studies: Enables exploration of genotype-dependent alternative splicing mechanisms using integrated RNA-seq and genotype data.
• Disease and complex trait research: Supports investigation of how genetic variation in splicing contributes to complex traits and diseases.

Methodology:

Integrates mapped RNA sequencing reads (BAM) with genotype data (VCF) and generates Sashimi, hive, and structure plots; implemented in Python and executed on Linux and Mac OS.