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

Lin, K. T., Krainer, A. R. (May 2019) PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis. Bioinformatics. ISSN 1367-4803

URL: https://www.ncbi.nlm.nih.gov/pubmed/31135034
DOI: 10.1093/bioinformatics/btz438

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

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Alternative Splicing
Investigative techniques and equipment > assays > RNA-seq
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA splicing
CSHL Authors:
Communities: CSHL labs > Krainer lab
Depositing User: Matthew Dunn
Date: 28 May 2019
Date Deposited: 29 May 2019 19:48
Last Modified: 29 May 2019 19:48
Related URLs:
URI: http://repository.cshl.edu/id/eprint/37982

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