Moore Notes 3 26 14

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Shotmap Working Group Call

  • Participants: Katie, Tom, Stephen, Stacia, Patrick, Guillaume
  • R21 microbiome temporal variation grant reviews were positive
  • Summary of project: slides
    • Collaborators
    • Goals
    • Existing solutions to functional analysis of metagenomes
      • Shotmap advantages: optimized read-length specific parameters, local, distributed, flexible, database organization
    • Statistical simulations
    • Empirical analyses
      • Re-analysis of Gilbert's English Channel data
        • Confirm main findings
        • Goods coverage low in transcriptomes with KOs but not with SFams
        • Differentially abundant families:
          • Transcriptomes differ from genomes
          • Oxidoreductases higher relative abundance in transcriptomes vs. genomes
          • Katie: try overall test and then pairwise
          • Patrick: try different multiple testing procedure or lumping families into groups to test first or modeling differences and looking for outliers
        • Clustering of temporal profiles: updated temporal variation slide
          • Patrick: Log transform, plot as heat map, order columns by covariates
          • Katie: Standardize by IQR
      • MetaHIT data
  • To do list and who can help
    • Tom: wrap up L4 analysis
      • Stacia: Can we analyze SEED to directly compare to Gilbert et al?
    • Stacia/Tom: Redo MetaHIT samples run by Patrick and Tim with optimized parameters
    • Stephen: Read-length specific parameters
    • Patrick/Tom: Time, memory, and space requirements (and how much db grows with each analysis), e.g., on HMP or T2D or GlucoseControl
    • Stacia: Software improvements: testing, data analysis tools, MicrobeCensus integration
  • Revisit this on April 9 or 16 call