RNASeq data sets available in Integrated Genome Browser

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RNASeq data sets available in Integrated Genome Browser

Loraine, Ann
Dear all,

Integrated Genome Browser now includes RNA-Seq data sets from Arabidopsis, maize, and sorghum.

To download the latest version of Integrated Genome Browser, visit: www.bioviz.org/igb

IGB is a desktop genome visualization tool mainly used to analyze and explore big data sets, such as read alignments from RNASeq experiments.

Two tutorials are available to help you get started visualizing RNASeq data (as alignments and coverage graphs) in IGB.

To view the tutorials, visit the IGB User's Guide:  http://wiki.transvar.org/confluence/x/K4DCAQ.

The tutorial titled "RNA-Seq coverage graphs" uses maize RNASeq data to show how coverage graphs can reveal new genes and differentially expressed genes. (If you are new to IGB, start with this one.)

The tutorial titled "Assessing splicing" explains how to use IGB to look for alternative splicing evidence in read alignments data.

There is also a simple, interactive tutorial describing basic navigation functions. To run the interactive tutorial, go to Help > Tutorials after launching IGB.

The currently available Arabidopsis RNASeq data set includes alignments and coverage graphs from a cold stress experiment performed here at UNCC. Information about the experiment is available from the main IGBQuickLoad site: http://igbquickload.org/quickload/A_thaliana_Jun_2009/cold_stress/.

For potential data providers:

IGB QuickLoad is a very simple data integration and sharing system IGB uses to combine data from multiple sites. If you have big data sets to share, you can add them to a QuickLoad section of your lab Web site and then publish the URL. IGB users can then enter the URL into IGB and see your data alongside other data sets (gene models, ESTs, TDNA insertions, RNASeq, etc) provided by other groups. You can also password protect the data if you want to keep it private prior to publication. So far as I know, none of the other desktop genome browsers support this; this is unique to IGB. However, they may adopt it as well – it is very simple and requires no specialized software.

If you are interested in trying this in your lab, the IGB team would be glad to provide advice and help, as this will help us improve the documentation and give us ideas for new features. More information about QuickLoad is here: http://wiki.transvar.org/confluence/x/0YIHAQ.


Ann Loraine

Ann Loraine, Ph.D.
Associate Professor
Department of Bioinformatics and Genomics
University of North Carolina at Charlotte
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
[hidden email]<mailto:[hidden email]>

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