RNAseqViewer:
Visualizing RNA-Seq data
RNAseqViewer let you visualize the various data from
the RNA-Seq analyzing process, for single or multiple samples. By
focusing on gene expression and transcript isoforms, the program offers
innovative ways to present the transcriptome data.
Top and bottom: splicing junction and read coverage from the output of TopHat. Middle: transcript assembly from Cufflinks. Colors depend on read count / FPKM.
Reads mapped to the genome, with mismatches against the reference genome in color. The hovered read pair is highlighted with additional data in a tool tip.
Heatmap view of reads FPKM from prostate cancer tumors and matched normal tissues, highlighting differential gene expression.
RNAseqViewer is a handy tool for
scientists who use RNA-Seq data to compare multiple transcriptomes,
for example, to compare gene expression and alternative splicing of
cancer samples or of different development stages.
Author: Xavier Rogé (rogex10@mails.tsinghua.edu.cn)
Contact: Xuegong Zhang (zhangxg@tsinghua.edu.cn)
MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, China (lab's website)
You are welcome to contact the authot for any question or suggestion!
Cite us!
Rogé Xavier and Zhang Xuegong. RNAseqViewer: Visualization tool for RNA-Seq data. Bioinformatics (2013). doi:10.1093/bioinformatics/btt649
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Program features
RNAseqViewer currently supports 7 types of data often used in
RNA-Seq analysis (see table 1). Different types
of view for each data set allow the visualization of different levels
of information, including heatmap-like views for informative and yet
very compact tracks, making possible to visualize dozens of samples
simultaneously.
The user interface has been design to enable smooth browsing of the
data. RNAseqViewer supports dynamic zooming and panning using the
mouse, the keyboard or the buttons of the interface. Direct access to
a specific position is possible by specifying coordinates or a gene's
name.
Special attention has been given to the memory management, so that
very large data sets can be visualized without exceeding memory limits
nor affecting the fluidity of the user interface.
Other features include the possibility to hide intronic regions,
the choice of the interface language (currently English, Chinese or
French) and the possibility to print out the graphs or to export to
PDF or image format.
RNAseqViewer has been coded in
Python, hence it is expected to
work on most platforms. It uses the programs
samtools and
PySide.
Table 1: Supported data types
| Type of data |
Format |
Views |
| Mapped reads |
SAM/BAM |
Reads, coverage, heatmap |
| Junctions |
BED |
Junction lines, junction reads |
| Transcriptomes |
GTF |
Expanded view, collapsed view |
| DNA sequences |
FASTA |
Nucleotides |
| Gene annotations |
RefFlat, GTF |
Expanded view, collapsed view |
| Numeric values |
Wiggle |
Histogram |
| Other tracks |
BED |
Expanded view, collapsed view |
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News
- November 11, 2013
- The article "RNAseqViewer: Visualization tool for RNA-Seq data" has been accepted for publication in Bioinformatics.
» See the abstract » See PDF article
- October 14, 2013
- Release of RNAseqViewer v0.8.0, including session saving, legends for colored graphs, speed improvement, inproved user manual and several bug fixes.
- July 8, 2013
- Release of RNAseqViewer v0.7.2. with several bug fixes and usage improvements.
- May 8, 2013
- Release of RNAseqViewer v0.7.1. This version fixes several bugs from the previous version.
- April 16, 2013
- Release of RNAseqViewer v0.7.0. This new version includes 1) a support for genome annotations in GTF, both uncompressed and compressed with BGZIP; 2) tool tips viewable in a dockable sub-window with links to reference websites; and 3) many bug fixes and minor improvements.
- April 7, 11-12, 2013
- A poster introducing RNAseqViewer is presented at RECOMB 2013 and the satellite workshop RECOMB-seq. You can download the PDF version
.
- March 20, 2013
- This web page is published and RNAseqViewer is publicly available for the first time, in version 0.6.
- February 26, 2013
- RNAseqViewer poster submission for RECOMB 2013 has been accepted. The poster will be presented at RECOMB and RECOMB-seq in early April 2013.
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Download RNAseqViewer v0.8.0
RNAseqViewer is written in Python 3 and makes use of some
additional libraries. Hence you have two options to run it. The first
one is to download the source code, install Python and the necessary
libraries, and run the
program as a Python script. The other and easier option is to download
the program as an executable which includes the Python interpreter and
the necessary libraries.
The source code and binaries are freely available for academic use.
Please read the
installation guide
and the illustrated quick start tutorial.
-
Windows 32bit installer (12 Mb)
Download and run the installer to install the program.
Tested on Windows XP pro SP3 and Windows 7 SP1.
-
Windows 64bit installer (13 Mb)
Download and run the installer to install the program.
Tested on Windows XP pro SP3 and Windows 7 SP1.
-
Ubuntu and openSUSE binaries (15 Mb)
Download and uncompress the package, then run the executable "RNAseqViewer".
Tested on Ubuntu 12.04 and openSUSE 12.2.
-
Debian binaries (16 Mb)
Download and uncompress the package, then run the executable "RNAseqViewer".
Tested on Debian 7.
-
Source code (0.3 Mb)
Download and uncompress the package, then run python3 RNAseqViewer.py.
You should have the following programs installed on your computer: Python 3, Samtools, Tabix and the library PySide for Python 3 (needed packages: core, GUI and SVG).
Tested on Windows 7, Ubuntu 12.04 and Debian 7 with Python 3.2, PySide 1.1.0, Samtools 0.1.12 and Tabix 0.2.5.
You can also download some sample data for testing purpose:
sample_data.tar.gz (12 Mb)
or sample_data.zip (13 Mb)
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