PSI-Sigma

"PSI-Sigma" is a computational tool to enhance the detection and reporting of alternative pre-mRNA splicing (AS) changes using a novel Percent Spliced-In (PSI) index. Recognizing the limitations of previous PSI-detection tools, which were constrained to specific AS events and evaluated predominantly through simulated RNA-seq data, PSI-Sigma leverages actual RNA-seq data from spliced synthetic genes (RNA Sequins) for benchmarking its performance against leading alternatives.

Key Features and Functionalities:

- Comprehensive AS Event Detection: PSI-Sigma extends beyond the capabilities of previous tools by efficiently detecting a wide range of AS events, including those with multiple alternative exons and intron-retention events.

- Benchmarked with Real RNA-seq Data: Unlike many other tools that rely on simulated data for evaluation, PSI-Sigma uses actual RNA-seq data from RNA Sequins, ensuring a more reliable assessment of its performance metrics, including precision, recall, false positive rate, and correlation.

- Applicability to Long-read RNA-seq Analysis: PSI-Sigma's utility is not limited to short-read RNA-seq data; it has also been briefly evaluated for long-read RNA-seq analysis using nanopore sequencing technology, showing its versatility in handling diverse sequencing data.