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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 3,289,962. Compare the results for different alignment programs and settings. Can you explain what's going on here?

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    Answer
    Answer

    There is a 16 base deletion in the gltB 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

If you've made it through the other exercises on your own data, take a look at some human genome re-sequencing data where the files can be loaded directly from public databases.

Advanced exercise: human data scavenger hunt 
Anchor
scavenger
scavenger

See this page for the human data scavenger hunt

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Is there an alternate allele in the child which correlates with one or both of the parents? (i.e. - do genetics work?)

From here...

 

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titleTo visualize mapped data without calling variants

You will need to index your reference FASTA and convert your SAM output files into sorted and indexed BAM files. The "why?" behind these steps is described more fully in the Variant calling tutorial. If you are in your mapping directory, these commands will perform the necessary steps.

Warning
titleSubmit to the TACC queue or run in an idev shell
Code Block
samtools faidx NC_012967.1.fasta
samtools view -b -S -o bowtie/SRR030257.bam bowtie/SRR030257.sam
samtools sort bowtie/SRR030257.bam bowtie/SRR030257.sorted
samtools index bowtie/SRR030257.sorted.bam

Repeat the last three commands for each SAM output file that you want to visualize in IGV.

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