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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 on your Desktop and double-clicking.
Load
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genome into IGV
From the main window of IGV, click on File -> Import Genome and you should be presented with the following window.
Enter the ID and Name of the Genome you are working with and select the path to your *.fasta file (the index, *.fai file needs to be in the same directory), then select the path to your *.gff file for the Gene File.
Load mapped reads into IGV
From the main window of IGV, click on File -> Load File. Choose bowtie.sorted.bam
Using IGV
After importing your reference genome and loading an alignment file, your screen should look similar to the following:
And you are now free to investigate different areas and their alignments in the genome.
Exercises
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- Try adjusting the options for viewing the data by right-clicking on the various tracks.