Moore Notes 8 6 14

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Group Call

  • Participants: Katie, Tom, Stephen, Patrick, Stacia, Dongying, Sarah, Guillaume
  • META Symposium
    • Talk summaries, stately
  • Sharpton lab
    • New postdoc: Chris Gaulke (from UC Davis)
    • Students
  • Shotmap authorship discussion
  • Stephen: slides
    • Simulation framework for evaluation of gene family relative abundance estimates from shotgun metagenomes
    • Mock communities with species abundance distributions from Bork/Weinstock paper
    • Translation methods affect performance and data volume/compute
      • Metagenomic gene prediction methods reduce data volume a lot and perform almost as well as six-frame translation
    • Comparison with MG-RAST
      • Shotmap annotates more KOs
      • Abundance estimates are correlated (on log scale), but there is disagreement
      • Working on annotating genomes in the simulation to have a gold standard for comparison
      • Suggestions: color by KO properties, quantify and then eliminate not-detected KOs
    • Other parameters evaluated:
      • Sequencing depth
      • Search method
      • Score threshold (versus e-values, which are >0 for huge dbs)