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- Jump to the next point of interest. Click on a track name on the left side of the window (Ex: bowtie.vcf), to select it. You can then use
control-fandcontrol-bto jump forward and backward within that list of features. Try this on the variant calls track. - Jump right to a gene. Type its name into the search box. Try "topA".
- Navigate more quickly. The
page-uppage-down,home,end. - Load multiple VCF and BAM alignments at once. Try this to compare a few different regions between the bowtie and BWA results.
- Change the appearance of genes. Right click on the gene track and try "expanded". Experiment with the other options.
- Change the appearance of reads. Right click on a BAM track and choose "show all bases" and "expanded". Experiment with the other options.
See the IGV Manual for more tips and how to load other kinds of data.
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?
- Go to coordinate 2,698,092. Compare the bowtie and BWA alignments. Can you explain what's going on here?
- Go to coordinate 475,263. ompare the bowtie and BWA alignments. What's the story here?
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