Downloads

• Source + doc
• Test files (355Mb)
• Source + doc + test files
• Files to reproduce website figures

The script in this package was designed by Marc Descrimes (contact: marc.descrimes@curie.fr).
The current implementation was written by Marc Descrimes and Yousra Ben Zouari.

Version: beta 1.1

This program is a free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Prerequisites

The script runs with R (>= 3.0.2).
R packages GenomicRanges and Rsamtools should be installed.
http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html

R is a multi-platform software, thus Ving works on any system where R can be installed.
Ving has been successfully tested on Ubuntu (>= 12.04.2), MacOSX 10.9 and Windows 7.
The provided documentation explains how to use Ving on a UNIX system.

Samtools should be up and running in order to create bam file indexes.
Index files must be in the same directory as bam files, with the default file name given by samtools.
Samtools are in the repositories of many distros. Go here for the freshest version:
http://samtools.sourceforge.net/

You should now be able to start using real data!

Examples of NGS signal visualization using Ving

Click here to download command lines and truncated bam and gff files used to produce the following figures.

• Small RNA-seq (yeast):

  
  
  Strand-specific “classic” visualization of 21-25 nt small RNA densities along the SPAC167.03c locus in rdp1D Schizosaccharomyces pombe control cells (vector) or cells overexpressing Dcr1. Signal from each library is shown in a separate panel. Reads mapped on the + and – strands are shown on the top and bottom sides of the 0 horizontal line, respectively (additional representation in different colors optional). Annotated genomic features are represented as “box” (ORF) and “line” (mRNA). Original data described in Yu et al. Mol Cell 2014, 53(2):262-276.

• ChIP-seq (RNAPII, yeast):

  
  
  Unstranded “line” visualization of RNAPII ChIP-seq profile along the YDL140C (RPO21) locus in a wild-type strain of Saccharomyces cerevisiae. Signal intensity for each library is represented by a different colored line (IP, black; input, green). Strands are as in the “classic” view. Annotated ORF are represented as “box”. Original data described in Van Dijk et al. Nature 2011, 475(7354):114-117.

• NET-seq (Rpb3, yeast):

  
  
  Strand-specific “line” visualization of the NET-seq profile along the same region as B in wild-type (black) and dst1D (red) cells of S. cerevisiae. Original data described in Churchman et al. Nature 2011, 469(7330):368-373.

• Total RNA-seq (yeast):

  
  
  Strand-specific “heatmap” visualization of the paired-end total RNA-seq signal along the YBR019C-YBR020W (GAL10-GAL1) locus in two biological replicates of S. cerevisiae wild-type cells grown in glucose- or shifted for 1 hour in galactose-containing medium. Distinct panels are used for each strand. In each panel, each lane corresponds to one library. Signal intensities range from white (low) to dark blue (high). Annotated ORF are represented as “box”. Original data described in Manfrini et al. EMBO Rep 2015, 16(2):221-231.

• Total RNA-seq (human):

  
  
  Strand-specific “heatmap” visualization of total RNA-seq signal along the HOTAIR locus in MCF-7, HeLa-S3 and NHLF cell lines. Annotated transcripts and exons are represented as “arrow” and “rectangle”. Original data from the ENCODE project described in Djebali et al. Nature 2012, 489(7414):101-108.