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See the IGV Manual for more tips and how to load other kinds of data.
Exercises
- Why are some reads different colors? Hint: Try changing the display options to show read pairs and editing some of the distance constraints.
- What is a typical mapping quality (MQ) for a read? Convert this to the probability that it is mismapped.
Expand title Remember the formula for a Phred quality score? The estimated probability that a read is mapped incorrectly is 10^(-MQ/10).
- Can you find a variant where the sequenced sample differs from the reference? This is going to be like looking for a needle in a haystack. Fortunately, we are going to learn how to use variant callers tomorrow and then we'll be able to zoom right to areas where there are discrepancies between reads and the reference genome that might indicate there were mutations in the sequenced E. coli.
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Tip: You can also index BAM and FASTA files the same way inside of IGV if you haven't already created indexes for them.
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. Compare the bowtie and BWA alignments. What's the story here?
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