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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
Hands On: Basic Analysis

On human chromosome 22,
which coding exons have
the most SNPs in them?
!
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
Exons, from UCSC

SNPs, from UCSC
Overlap pairings

1	

1	

2

Exon overlap counts
1	

1	

2

Exon overlap counts
Exons, from UCSC
1	

1	

2

Exon overlap counts
Exons, from UCSC
1	

1	

2

0	

0	

0

Join on exon name
1	

1	

2

Exon overlap counts
Exons, from UCSC
1	

1	

2

0	

0	

0

1	

1	

2

Join on exon name

Rearrange columns w/
cut
Your turn
http://usegalaxy.org/galaxy101
!

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