Moore Notes 11 3 10

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Group Call

  • phylOTU resubmission
    • bug fixed
    • new simulation analyses done
      • SILVA simulations
        • more divergent from reference library
        • more reads
        • accuracy is still pretty good - threshold for optimized performance is 0.15
    • GOS reanalysis is almost done
    • manuscript will be done by next Monday - resubmit by next Friday (got extension)
  • AMPHORA2 and OPF db/read classifier
    • AMPHORA2 will meet outcomes from original proposal by making a gene family tool for more families
      • Donying's additional markers
      • Eukaryotes
      • Viruses - coordinate with Peter Skewes-Cox in DeRisi lab
    • Other modules for read classification and OPFs
    • glocal alignment issues in HMMR3
  • niche-mapping paper
    • Josh wrote up methods - document sent by email
      • Environmental layers carefully chosen
      • Dealt with sampling bias issue
      • MESS plots: Figure 1 shows that our data set does a good job of covering the global environments
    • Bootstrap values from RDP - what cutoff to use for a taxon call?
      • RDP gives a designation across hierarchy of taxa with bootstrap scores
      • Known sequences get bootstrap values in 90-100% range
      • Shotgun sequences from Rebecca's HMP analysis is bimodal with dip at 80% and peaks at 70% and 95%
      • Steve: 50% cutoff down to genus level in Claesson et al.
      • Should look at how results depend on changing cutoff and/or taxonomic level used
    • JG: diversity gradients at different taxonomic levels in literature - will send papers
    • Dividing up writing - separate call to plan