Moore Notes 9 18 13

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Group Call

  • Participants: Katie, Jonathan, Dongying, Guillaume, Sarah, Ladan, Josh, Stephen, Tom
  • Morgan Langille got a faculty job at Dalhousie
  • Dongying's marker paper will be published in PLoS ONE
  • Josh will talk to Alexis in next week about Tara oceans sampling
  • Tom talked to Morgan about PICRUSTs
    • We would need to thoroughly vet its application to marine communities
    • Good idea to compare shotgun metagenome protein abundances vs. PICRUSTs estimates
    • Limited to taxa in the GreenGenes Db
    • Limited to proteins families in KEGG (or you need to annotate genomes with your protein db)
    • Doesn't do any correction for genome length, unannotated proteins, etc.
    • Jonathan: Marine is probably the next best place to go due to GBMF funded genome sequencing
    • Guillaume & Tom want to start with English Channel L4 dataset
      • Need to annotate with KEGG (did SFams already)
      • Guillaume is compiling the 16S from same samples and running it through PICRUSTs
    • Caveat: 454 sequencing, so lower coverage than enteric samples in PICRUSTs paper
  • Stephen has been exploring normalization of protein family abundance measurements
    • Adjust for number of genomes in the community
      • To account for coverage of proteins in community by db
      • Also to adjust for genome size
    • Ground truth with Dongying's marker genes
    • Caveat: doesn't account for archaea or eukaryotes very well right now, but could in future
      • Tree of Life project has eukaryotic (protist) marker genes - universal, but not necessarily single copy
      • Still won't know average genome size very accurately