WBConfCall 2015.05.07-Agenda and Minutes

From WormBaseWiki
Jump to navigationJump to search

Agenda

Assembly of CB4856 (Hawaiian) strain

LeDeana Hillier is about to publish a full assembly of CB4856. She has also produced an alignment against (an old version of) the N2 reference, and proposes to submit it to WormBase. Questions:

  • Should we host the assembly of CB4856 as a genome in its own right? Or should we do as we've always done, and use the data to add to the variation set for CB4856 (which currently comprises data from numerous studies)?
  • If we want to host the genome in its own right, should we attempt to annotate it? It would be fairly straightforward to project the N2 gene models across, but should we go further than that, and curate known cases where the gene structure in wild isolates if different from N2? Should we use the same WBGene ids for the genes in CB4856 or add new ones?
  • More generally, what are the use-cases of this data set?

WormMethod chapters

  • Submission status?

ParaSite/WormBase streamlining

  • we removed the parasitic T3 worms from WormBase
  • the parasite orthologs are therefore not accessible from the C.elegans genes
  • for the 3 worms that are in ParaSite and WormBase (O.volvulus/S.ratti and B.malayi) it is not easy to switch between the sites to access data the respective other is missing

RNA Central Identifiers

  • What is the current status for WB wrt incorporating RNA Central IDs?

Minutes

Assembly of CB4856 (Hawaiian) strain

  • Kevin - LeDeana Hillier wants WormBase to do something with Hawaiian strain.
  • Currently false positives, her data is cleaner.
  • Create new Variation objects or treat as separate genome ? Deserves separate genome.
  • Make haplotides indexable.
  • If we have 25 strains with individual sequence variants, can we donwload ? Not now.
  • First ftp for downloading genome.
  • Can easily freeze as separate genome, and project reference genome. FASTA and GFF files.
  • Make tool to give equivalent alignment from reference region to a 10kb region in N2. Would be easier in genome browser, but separate tool okay for now.
  • How to deal with variations if not identical ? Can see in genome browser beforehand.
  • Would be easy to add to Jbrowse and Gbrowse if the tool existed.
  • What can we do easily ? Pull in genome, first-pass annotate, make a genome browser. Can somehow make the alignment available.
  • Is this one-off, or will we have more like these ? This one is particularly interesting, community interest around it, don't know about others.

WormMethod chapters

  • Paul S - Are people happy with WormMethod chapters, have people looked at other people's ?
  • People still looking. Deadline was last week. Paul S will look through them again in a week and a half.

ParaSite/WormBase streamlining

  • Michael P - removed parasitic T3 worms from WormBase.
  • Use toggle button to switch between WormBase/ParaSite gene pages.
  • How to search ? Separate way to go to each site, by default go to the species-specific site.
  • Can we link from WormBase to Parasite and viceversa ?
  • Give webteam dump of Parasite data to index ? Sounds good, currently using acedb format. Try homologs as starting point. Will look at current xml structure.

RNA Central Identifiers

  • Should be in WormBase by next release.

International meeting giveaways

  • Give aways for next meeting will be more bags with new logo and Parasite. People liked bags. Waiting for design.
  • Do we have official logos ? Yes in svg and png, send to Caltech.