Moore Notes 8 25 10

From OpenWetWare
Jump to navigationJump to search

Group Call

  • Introduce Rebecca Lamb
  • 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