Visualization using Integrated Genome Viewer (IGV)

Overview

The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.

Get your data

We are going to look at two mapping results- for samples C1_R1 and C2_R2.  We can download the corresponding bam files and index files by either scping them over from lonestar5 to your computer. Or I have placed them in a convinient web server. Download the corresponding bam files and index files from here onto your computer.

Get a couple of .bam and .bai files (for a given sample, you'll need both .bam and .bai files) from the hisat mapping results here:
 Within your scratch directory, under my_rnaseq_course/day_3_partA/gene_counting_exercise/hisat_results/

Some useful IGV Features

1. SNPS
   
2. Coverage tracks- to see coverage in one sample vs another acorss a certain location.
3. All sorts of views for paired end data.  These help us find analogous pair mappings, split mappings etc.
   
   
   

Launching IGV

There are two ways; Launching IGV in your web browser or by downloading the binaries locally and running IGV from your machine. We are just going to run it from web browser for this demo.

In a Web browser

Navigate a web browser to this page:http://www.broadinstitute.org/software/igv/download. You will need to register your email address to use this option!

Go ahead and click on the "Launch with 2 GB" option. This will download a "Java Web Start" file that you can launch by locating it on your Desktop and double-clicking.

Locally on a Mac or Windows computer

Use this link to download IGV:

http://www.broadinstitute.org/software/igv/download

If this is not working, you might need to try the web start.

Load genome track on IGV

From the main window of IGV, click on Genomes > Load Genome from server....  Choose dm3  Because our genome is already on the IGV server, we can do this.

Load mapped reads into IGV

From the main window of IGV, click on File > Load from File.... Choose your bam file.

After loading the reference genome and loading an alignment file, click on the + button in the upper right until reads appear! 

Look at one of the differentially expressed genes on IGV

Some of the top upregulated genes  were:

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