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SplicePlot: a utility for visualizing splicing quantitative trait loci
Summary: 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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967110/ https://www.ncbi.nlm.nih.gov/pubmed/24363378 http://dx.doi.org/10.1093/bioinformatics/btt733 |
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author | Wu, Eric Nance, Tracy Montgomery, Stephen B. |
author_facet | Wu, Eric Nance, Tracy Montgomery, Stephen B. |
author_sort | Wu, Eric |
collection | PubMed |
description | Summary: 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. Availability and implementation: Source code and detailed documentation are available at http://montgomerylab.stanford.edu/spliceplot/index.html under Resources and at Github. SplicePlot is implemented in Python and is supported on Linux and Mac OS. A VirtualBox virtual machine running Ubuntu with SplicePlot already installed is also available. Contact: wu.eric.g@gmail.com or smontgom@stanford.edu |
format | Online Article Text |
id | pubmed-3967110 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-39671102014-04-18 SplicePlot: a utility for visualizing splicing quantitative trait loci Wu, Eric Nance, Tracy Montgomery, Stephen B. Bioinformatics Applications Notes Summary: 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. Availability and implementation: Source code and detailed documentation are available at http://montgomerylab.stanford.edu/spliceplot/index.html under Resources and at Github. SplicePlot is implemented in Python and is supported on Linux and Mac OS. A VirtualBox virtual machine running Ubuntu with SplicePlot already installed is also available. Contact: wu.eric.g@gmail.com or smontgom@stanford.edu Oxford University Press 2014-04-01 2013-12-19 /pmc/articles/PMC3967110/ /pubmed/24363378 http://dx.doi.org/10.1093/bioinformatics/btt733 Text en © The Author 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Wu, Eric Nance, Tracy Montgomery, Stephen B. SplicePlot: a utility for visualizing splicing quantitative trait loci |
title | SplicePlot: a utility for visualizing splicing quantitative trait loci |
title_full | SplicePlot: a utility for visualizing splicing quantitative trait loci |
title_fullStr | SplicePlot: a utility for visualizing splicing quantitative trait loci |
title_full_unstemmed | SplicePlot: a utility for visualizing splicing quantitative trait loci |
title_short | SplicePlot: a utility for visualizing splicing quantitative trait loci |
title_sort | spliceplot: a utility for visualizing splicing quantitative trait loci |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967110/ https://www.ncbi.nlm.nih.gov/pubmed/24363378 http://dx.doi.org/10.1093/bioinformatics/btt733 |
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