Moore Notes 3 16 15

Group Call

• Participants: Katie, Tom, Patrick, Stephen, Ladan, Josh, Sarah

• Tara Oceans analysis:
  • Running samples (Stephen)
    • Stephen found a bug in rapsearch (authors looking into it)
    • Tom will conduct a run with old version and shotmap batching
  • Filter sizes (Josh)
    • Five different sizes (overlapping)
    • Most sizes not done at most geographic locations (example)
    • Size 0.22 to 3.0 is most common, 0.22 to 1.6 used in other locations
    • Confounded with location, so cannot model out
    • Stephen: filter size is positively correlated with average genome size
    • Josh will spot check for any missing files and summarize
  • Powers et al. (2015) natural products paper http://elifesciences.org/content/4/e05048
    • Used eSNaPD: http://esnapd2.rockefeller.edu
    • Patrick: coverage may be lower in non-targeted Tara Oceans data
    • Tom: disentangling taxonomic signal would be a good idea
    • Tom: look at hits on a gene family phylogeny
    • Josh: places with highest level (>1% of reads) of each gene family cluster
      • But should not be called "hotspots" since only at sample locations and not global
      • Survey gap analysis: predicting where to sample to find different functions from previously known
    • Which protein families and marine systems to focus on?
      • Quorum sensing (too diverse?)
      • KS domains good because same domain used for many different functions
      • Non-ribosomal peptide synthesis
      • Peter Dornstein: mass spec database (BLAST for peak profiles) to prioritize

• Next calls
  • March 30: Patrick
  • April 13: Tara Oceans and Sharpton lab clade diversity project