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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.
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Load data into IGV
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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.
Preparing alignment file.
If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping (bowtie, BWA).
Convert to BAM format.
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samtools sort -bS input.sam output.bam
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Sort.
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samtools sort input.bam sorted_output
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Note: The second parameter passed here is a prefix and will be suffixed with .bam by samtools.
Index
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samtools index input.bam
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Import to IGV.
From the main window of IGV, click on File -> Load from File and select your input.bam file.
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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