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Integrative Genomics Browser

(http://www.broadinstitute.org/igv/)

Integrative Genomics Browser (IGV) is a third party software that enables the visualization of the coverage of the reference genome by transcripts and to qualitatively compare coverage for various experimental conditions.

First, click on “Launch IGV” button : users can use this one from the RNA-Seq homepage or from Read Count and DESeq Analysis pages.

The first window appears with a lower part already displaying the annotations of the reference genome (see below).

igv1.png (PNG)

Section #1 contains genome annotations. Colors corresponding to a specific genomic object are:

  • red : CDS
  • yellow : fCDS
  • green : tRNA
  • blue : rRNA, miscRNA

To see genome coverage, users can load data in the drop down menu “File/Load from Server”.
A list of available datasets for import will then appear in a new window. Tick the checkbox corresponding to the experiments to load in the browser and click “OK”.

igv2.png (PNG)

Warning: The loading process may take a while, so please be patient!

The, the coverage is visible :

igv3.png (PNG)

Users can also organize the display :
Example : to compare the same type of experiment user can group forward and reverse experiment. (just click and drag)

igv4.png (PNG)

Users can enlarge the view by drag’n dropping the mouse on the area of interest.

igv5.png (PNG)

It is possible to zoom in to see gene sequence and translation.