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PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis.

ABSTRACT:

Motivation

Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data. We developed PSI-Sigma, which uses a new PSI index, and we employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins) to benchmark its performance (i.e. precision, recall, false positive rate and correlation) in comparison with three leading tools (rMATS, SUPPA2 and Whippet).

Results

PSI-Sigma outperformed these tools, especially in the case of AS events with multiple alternative exons and intron-retention events. We also briefly evaluated its performance in long-read RNA-seq analysis, by sequencing a mixture of human RNAs and RNA Sequins with nanopore long-read sequencers.

Availability and implementation

PSI-Sigma is implemented is available at https://github.com/wososa/PSI-Sigma.

SUBMITTER: Lin KT

PROVIDER: S-EPMC6901072 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis.

Lin Kuan-Ting KT Krainer Adrian R AR

Bioinformatics (Oxford, England) 20191201 23

<h4>Motivation</h4>Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data. We developed PSI-Sigma, which uses a new PSI index, and we employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins) to benchmark its performance (i.e. precision, recall, false positive rate and correlation) in comparison with three lead ...[more]

PMID: 31135034

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