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Agenda: second half of the day

Bioinformatics runs and workflows	

!

Overview of the Galaxy project	

!

Tailoring a Gala...
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 exon...
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/
c...
Your turn
http://usegalaxy.org/galaxy101
!
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Galaxy workshop

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Transcript of "Galaxy workshop"

  1. 1. 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
  2. 2. Hands On: Basic Analysis On human chromosome 22, which coding exons have the most SNPs in them? !
  3. 3. 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
  4. 4. Exons, from UCSC SNPs, from UCSC
  5. 5. Exons, from UCSC SNPs, from UCSC Exons, from UCSC SNPs, from UCSC Overlap pairings
  6. 6. Exons, from UCSC SNPs, from UCSC Exons, from UCSC SNPs, from UCSC Overlap pairings 1 1 2 Exon overlap counts
  7. 7. 1 1 2 Exon overlap counts Exons, from UCSC
  8. 8. 1 1 2 Exon overlap counts Exons, from UCSC 1 1 2 0 0 0 Join on exon name
  9. 9. 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
  10. 10. Your turn http://usegalaxy.org/galaxy101 !
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