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Viewing reads - the basics

You should now have load some data into IGV (if not, go and do that now.) You'll probably see something like this:

To see the reads you will need to zoom into a location on the genome. For example, let's zoom into the gene that harbours the famous chloroquine resistance mutation, Chloroquine resistance transporter (CRT). To search for it you will need its ID, which is PF3D7_0709000. Voila! Some reads.

IGV hints

This is a good point to try a few options to get used to IGV.

  • For paired-end data, try the 'view as pairs' option. It can be found in the context menu, obtained by right-clicking anywhere on the track.

  • If you don't like how reads are displayed, try 'collapsed', 'expanded', or 'squished' from the context menu. Which one do you like best?

  • Try clicking on a read. What is all that info? Where does it come from? What does it mean?

  • Try moving around and zooming in/out.

  • There's also a genes track - it can be annoying when it is squished. Try right-clicking and choose 'expanded' to see the genes.

Basics​

Scroll around a bit to look at the reads.

Can you find:

  • a sequencing error?
  • a SNP?
  • an insertion / deletion variant?

What makes you sure that's what these are?

Note

By default you are looking at all reads (including those that didn't map very well.) There's an option hidden away under Preferences -> Alignment that lets you set a mapping quality threshold. A good default value to put here is 20 (but remember that by doing this you are filtering out some reads!)