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

KuanTing Lin | Zendy; Adrian R. Krainer | Zendy

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

Author(s) -

KuanTing Lin,

Adrian R. Krainer

Publication year - 2019

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btz438

Subject(s) - intron , rna , benchmark (surveying) , rna seq , computational biology , in silico , computer science , rna splicing , false discovery rate , nanopore sequencing , exon , gene , biology , genetics , genome , transcriptome , gene expression , geodesy , geography

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).

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