Brendel Group Presentation: 5 Nov 2013

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Slides from my debriefing of the Cold Spring Harbor Lab Genome Informatics meeting I attended 30 Oct-2 Nov 2013.

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Brendel Group Presentation: 5 Nov 2013

  1. 1. CSHL Genome Informatics: debriefing Daniel S. Standage, 5 Nov 2013 
  2. 2. Themes  RNA-Seq  Genomic variation  Technical details matter  Reproducibility  Web-based tools
  3. 3. RNA-Seq  De novo assembly  Sreeram Kannan, Lior Pachter, David Tse  Bayesembler  Quantification  Sailfish  Lior Pachter?
  4. 4. Genomic variation  MedSavant  GEMINI  SCALPEL: indel ID via NGS  Others  Genome rearrangements  SNPs
  5. 5. Technical details matter  Reproducibility  Software engineering  Cyberinfrastructure  Clear description of methods
  6. 6. Software engineering protips  Version everything  Test everything (and automate those tests)  Review everything  Measure everything  Engage users
  7. 7. Reproducibility  Don’t rely on a single assembly  Don’t rely on a single source of annotation  Genome sequenced twice at deep (60x) coverage, variants ID’d; only 94% agreed
  8. 8. Web-based tools  Utilize ubiquitous browser  Most are open source, some offer VM distro  APIs and SDKs  integration  extension  programmatic access
  9. 9. A few talks of interest  Mario Stanke: comparative gene finding  Lior Pachter: RNA-Seq methods, units  Michael Snyder: integrative “Snyderome”  Sreeram Kannan: RNA-Seq assembly  Rob Patro: Sailfish  Chung-chao Hon: natural antisense transcripts

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