Moore Notes 1 15 10

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OTU group call: JG, SK, KP, TS, SR, JL

  • Mitch Sogin manuscript
    • JG: looks at three attributes that affect OTU estimation
      • PCR/seq error,
      • multiple seq alignment (overestimates) vs. pairwise,
      • linkage method in clustering (furthest neighbor overestimates), prefer average linkage
    • Analyze a bunch of data sets where they know the truth (experimental mixtures, or single species)
    • TS: how does it affect us?
      • pairwise alignment isn't an option for us.
      • user needs to quality control sequencing data prior to our pipeline (sequencing, but not PCR could be issue for metagenomics)
  • Paper planning
    • What is novel in our work?
    • What will be cited? (Software? Paper?)
    • Do we hit a novel part of the biosphere?
    • Data comparison idea: PCR vs. metagenomic 16S from GOS
    • Chao or similar for upper bound and estimate how much underestimation going on out there in different data sets
    • May need simulations
      • how to compare distance matrices, beyond path difference (need to account for the fact that there are metric distances)
  • To do list
    • Trees OK? Simulations (Sam with help from Tom & Steve on distance matrix evaluations, ecological evaluations)
    • Package code (Tom)
    • Code performance improvements (Tom)
    • Data analyses: (Tom and Steve will do some planning, maybe Josh and James can turn the crank once code is ready)
      • Re-analyze some other people's data sets?
      • PCR vs. metagenomic data analysis in GOS
      • Analyze new data sets (e.g. Quince et al data sets, what's new on CAMERA?, diversity map using all data sets we can find if enough)
      • Is diversity being underestimated? How much?