Moore Notes 12 2 09

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Subgroup Call

  • OTUs
    • version 1 of pipeline is done!
      • Sam's simulation results might lead to modifications
      • JE will talk to CAMERA: Tom will follow up Thurs
    • JE's question about FastTree
      • FastTree psuedo-counts method (with max=3.0) and mutual overlap with a third sequence account for non-overlapping reads
        • Sam: we need to emulate this in the simulation analyses
      • we use phylogenetic not sequence distance in MOTHUR
      • Tom will follow up
    • JG: Sogin and Welch talk
      • did simulations to show that MOTHUR generates too many clusters with large pyrosequencing data sets
      • new algorithm: pairwise alignment rather than multiple alignment
    • James is using OTUs (computing metrics)
      • posted raw and reformatted output of MOTHUR on edhar (see email)
      • lots of noise: big variation in number of reads and number of OTUs across sites
    • Josh: do we still need the wrapper script?
      • not essential right now
      • good to have for pipeline
    • publication on pipeline
      • focus on the identification of OTUs?
        • maybe interesting if we did a whole bunch of datasets
      • probably need software (CAMERA? Just Perl module OK for pub?)
      • and/or James (Josh's?) analyses
      • include simulations, e.g. just split up reference sequences
      • comparison with Biers et al. results, Sogin paper? Jenna's data?
  • Simulations
    • Sam has simulated data on genbeo
      • for a reference db with 20 sequences (5 chosen by maxPD, 15 randomly)
      • all parameters on wiki
      • 5 repeats of each combination
      • this makes a lot of data sets
      • directory name gives the details, within directories the names are the same (keep separate)
      • will reorganize and put on edhar
    • Tree building
      • which methods? RAxML (two ways), FastTree, pplacer (?)
      • which models?
        • WAG (in AMPHORA) vs. JTT (more like FastTree)
        • cat/cat+gamma
    • Next steps
      • Sam will make a wiki page with assignments
      • Steve: let's set up name conventions (Sam will do)
      • Sam will keep track of data sets that have same parameter values due to rounding
      • Steve: should share code/scripts over svn
      • Tom: data should be in svn too