Galaxy workshop

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