Content Comparison

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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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Load variant calls into IGV

We're really interested in places in the genome where we think there are mutations. You can load the VCF file, but first you need to index it.

1. Choose File -> Run igvtools....
2. Choose "index" from the commands drop-down menu.
3. Select your *.vcf file (Ex: bowtie.vcf) for "Input File"
4. Click the "run" button.

It will look like nothing has happened, but you can now close the window and choose File -> Load File. If you navigate to your IGV directory you will now have a brand new bowtie.vcf.idx file. You can now select bowtie.vcf and it will show up as a new track at the top of your window.

Tip: You can index BAM and FASTA files the same way if you haven't already created indexed for them.

Navigating in IGV

There are a lot of things you can do in IGV. Here are a few:

• Click on a track name on the left side of the window (Ex: bowtie.vcf), then it will be selected. You can then use control-f and control-b to jump forward and backward within that list of features. Try this on the variant calls.
• You can jump right to a gene by typing its name in to the search box. Try "topA".
• The home and end keys jump a page backward and forward.
• You can load multiple VCF and BAM alignments at once. Try this to compare a few different regions between the bowtie and BWA results.

Exercises

• Check out the rbsA gene region? What's going on here?
• What is going on in the pykF gene region? You might see red read pairs. What does that mean?