VING: a software for visualization of deep sequencing signals

BMC Research Notes
Marc DescrimesAntonin Morillon

Abstract

Next generation sequencing (NGS) data treatment often requires mapping sequenced reads onto a reference genome for further analysis. Mapped data are commonly visualized using genome browsers. However, such software are not suited for a publication-ready and versatile representation of NGS data coverage, especially when multiple experiments are simultaneously treated. We developed 'VING', a stand-alone R script that takes as input NGS mapping files and genome annotations to produce accurate snapshots of the NGS coverage signal for any specified genomic region. VING offers multiple viewing options, including strand-specific views and a special heatmap mode for representing multiple experiments in a single figure. VING produces high-quality figures for NGS data representation in a genome region of interest. It is available at http://vm-gb.curie.fr/ving/. We also developed a Galaxy wrapper, available in the Galaxy tool shed with installation and usage instructions.

References

Dec 20, 2000·Bioinformatics·K RutherfordB Barrell
Oct 9, 2002·Genome Research·Lincoln D SteinSuzanna Lewis
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Jan 21, 2011·Nature·L Stirling Churchman, Jonathan S Weissman
Sep 8, 2012·Nature·Sarah DjebaliThomas R Gingeras
Jan 1, 2014·Molecular Cell·Ruby YuDanesh Moazed

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Citations

Nov 17, 2019·Life Science Alliance·Marina PinskayaAntonin Morillon
Mar 7, 2019·Scientific Reports·Alexei SlesarevColette Cote

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Datasets Mentioned

BETA
GSE63444
SRA030505

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
RNA-seq

Software Mentioned

R
Windows 7
Unix
BEDtools
IGV
GenomicRanges
MacOSX
Gviz R package
gff
Gbrowse

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