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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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 versionPoster about RNAseqViewer presented at RECOMB 2013.
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.

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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User manual

The user manual can be accessed from the application at any moment, in the Help menu.

Alternatively, you can acces the on-line user manual or download the PDF version.

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