Agenda: second half of the day

Bioinformatics runs and workflows !

Overview of the Galaxy project !

Tailoring a Galaxy on the Cloud instance with new tools from the Galaxy Tool Shed

On human chromosome 22, which coding exons have the most SNPs in them?

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Hands On: Basic Analysis

A Rough Plan

• Get some data

• Coding exons on chromosome 22

• SNPs on chromosome 22

• Mess with it

• Identify which exons have SNPs

• Count SNPs per exon

• Visualize our results

Exons, from UCSC SNPs, from UCSC

Exons, from UCSC SNPs, from UCSC

Exons, from UCSC

SNPs, from UCSC

Overlap pairings

Exons, from UCSC SNPs, from UCSC

1 1 2

Exons, from UCSC

SNPs, from UCSC

Overlap pairings

Exon overlap counts

Exons, from UCSC

1 1 2

Exon overlap counts

Exons, from UCSC

1 1 2

Exon overlap counts

1 1 2

Join on exon name0 0 0

Exons, from UCSC

1 1 2

Exon overlap counts

1 1 2

Join on exon name0 0 0

1 1 2

Rearrange columns w/ cut

Your turn http://usegalaxy.org/galaxy101

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