Moore Notes 12 12 12

From OpenWetWare
Jump to navigationJump to search

Group Call

  • Participants: Katie, Jonathan, Stephen, Josh, Guillaume
  • Progress report due 1/15 (2 page update)
    • Assigning sections
    • Summaries due to Katie by 1/10
  • Josh update on beta diversity
    • Running now on cluster (same 16S data as submitted alpha diversity paper)
    • Preliminary maps by next Wednesday
  • Guillaume update on duplicate assignments of sequences in SFams
    • Doesn't seem like a sequence can be assigned to two families in current code
    • But ~120 duplicate sequences did get different assignments
    • Fix: keep older assignment, adjust newer families accordingly (new HMMs, trees, alignments)
    • Solution: going forward duplicates will be dropped before clustering and classification into existing families
  • Jonathan wants to go beyond constructing families
    • Initiated project several years ago to have diverse, automatically updated families
    • Can some one else take on this responsibility?
      • Looking around for groups that are doing regular updates
      • People are doing this for genomes
      • Use their family definitions, add our HMMs, trees
      • What about metagenomes?
      • In original CAMERA proposal
    • Good to tie our work to familiar and commonly used families
    • Stephen: advantage of SFams is that we could integrate family-specific membership thresholds for metagenomics data
  • Coordinating efforts with PhyloSIFT efforts (Aaron, E Matsen NSF grant)
  • Plan some in person meetings in 2013