Content Comparison

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You can start this tutorial two ways:

1. If you have an intro_to_mapping directory with output from the Mapping tutorial or the Variant calling tutorial, then you should use those files for this tutorial.
2. If you do not have any results, you can use some "canned" ones that we provide. Copy the entire contents of this directory back to your local machine:

   Code Block
   $BI/ngs_course/intro_to_mapping/IGV

   Then skip down to #Launching IGV.

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• 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. Compare the bowtie and BWA alignments. What's the story here?

Advanced exercise: human data scavenger hunt

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