SplicePlot: a utility for visualizing splicing quantitative trait loci | Zendy

Eric Wu | Zendy; Tracy Nance | Zendy; Stephen B. Montgomery | Zendy

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SplicePlot: a utility for visualizing splicing quantitative trait loci

Author(s) -

Eric Wu,

Tracy Nance,

Stephen B. Montgomery

Publication year - 2013

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/btt733

Subject(s) - python (programming language) , rna splicing , quantitative trait locus , visualization , source code , computer science , biology , documentation , population , computational biology , genetics , data mining , rna , gene , programming language , demography , sociology

RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility that produces intuitive visualization of sQTLs and their effects. SplicePlot takes mapped RNA sequencing reads in BAM format and genotype data in VCF format as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure.

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