Content Comparison

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• Check out the rbsA gene region? What's going on here?

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  Answer Answer
  There was a large deletion. Can you figure out the exact coordinates of the endpoints?

• Navigate to coordinate 475,288. Compare the bowtie, BWA, and bowtie2 alignments. Can you explain what's going on here?

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  Answer Answer
  There is a 16 base deletion in the gltA gene reading frame.

• What is going on in the pykF gene region? You might see red read pairs. What does that mean? Can you guess what type of mutation occurred here?

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  Answer Answer
  The read pairs are discordantly mapped. There was an insertion of a new copy of a mobile genetic element (an IS150 element) that exists at other locations in the reference sequence.

Workflow 2: Viewing Human Genome Data in IGV

Advanced exercise: human data scavenger hunt

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scavenger scavenger

Data from the CEU trio from the 1000 Genomes Project can be found directly from the Broad's server for IGV.

Find the dbSNP accession number for the SNP apparent in the two 1000 genomes project trios in the intron between exons 8 and 9 of the GABBR1 gene.

Steps:

1. Download and install the Integrative Genome Viewer from the Broad Institute.
2. Select "Human hg18" as the reference genome
3. Get some data: File -> “Load from Server…” -> 1000 genomes -> CEU and YRI trios
4. Navigate to the GABBR1 gene and the rightmost exons
5. Zoom in until you find the SNP
6. Load and look at the SNP track: File -> Load from server -> Annotations -> Variants -> dbSNP

This is whole genome coverage data; later we'll look at exome data.

From here...

You can also use IGV to visualize RNA-seq data in later tutorials.

Check out alternative genome browsers:

• Tablet - a lightweight NGS data browser