[Arabidopsis] RNASeq data sets available in Integrated Genome Browser

Loraine, Ann via arab-gen%40net.bio.net (by Ann.Loraine from uncc.edu)
Fri Jun 22 07:33:19 EST 2012


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.bio=
viz.org/igb

IGB is a desktop genome visualization tool mainly used to analyze and explo=
re 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.or=
g/confluence/x/K4DCAQ.

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

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

There is also a simple, interactive tutorial describing basic navigation fu=
nctions. To run the interactive tutorial, go to Help > Tutorials after laun=
ching IGB.

The currently available Arabidopsis RNASeq data set includes alignments and=
 coverage graphs from a cold stress experiment performed here at UNCC. Info=
rmation 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, y=
ou can add them to a QuickLoad section of your lab Web site and then publis=
h the URL. IGB users can then enter the URL into IGB and see your data alon=
gside other data sets (gene models, ESTs, TDNA insertions, RNASeq, etc) pro=
vided by other groups. You can also password protect the data if you want t=
o 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 =96 it is very simple and requires no specialized sof=
tware.

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

Sincerely,

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
704-250-5750
aloraine from uncc.edu<mailto:aloraine from uncc.edu>
http://www.transvar.org
http://www.bioviz.org
http://www.uncc.edu



More information about the Arab-gen mailing list