Moore Notes 8 25 10

Group Call

• Introduce Rebecca Lamb

• ISME meeting
  • Kelly's event
  • Meeting with Kelly on Friday
  • Tom's notes: http://friendfeed.com/isme13

• CAMERA 2.0
  • JE is testing workflows, e.g., RAMMCAP ("metagenomic annotation and clustering")
  • Interface is slow
  • Seems to work OK, better than previous iterations

• Updates
  • Sam
    • Simulating data from 16S and several proteins (rpoB, rpsB, one non-AMPHORA) to be processed similarly: filtering alignments, trees, tree comparisons
      • AMPHORA steps and Tom's filtering differ. Also alignment methods differ (INFERNAL vs. HMMR).
      • JE: better to do information content, not size
      • 70% coverage of profile or read helps ensure some overlapping reads
      • SK: mask columns based on reference sequences only, drop short reads (e.g., <100bp)
    • Suggestions for a non-AMPHORA protein: Gerstein lab membrane proteins, Xun Gu paper
    • Packaging up simulation code: SK will try to install as a test
  • Alex
    • 16S from human body sites (Rob Knight paper)
    • OTUs at different cutoffs vs. ecotype simulation
    • Are either linked to body habitat (microdiversity)?
      • Fisher's exact test for each habitat
    • Are ecotypes more associated than OTUs?
      • How to compare OTU vs. ecotype results?
    • Comparing the ecological inferences. How often is this done in the literature?
  • Martin/Steve
    • Want to simulate data sets, grab 16S sequences, estimate copy number
    • Sam's pipeline will do this by changing abundance distribution to be non-uniform

• Next group call: 9/8
  • GOS pow-wow