Hinxton 2016.01- Meeting minutes

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January 08, 2016

In attendance: KH, PD, GW, BB, JL

Curation

  • Reviewing "known" genes with poor gene models
    • PD and GW reviewing genes with a GCG name but questionable gene model
    • Many/most of these are members of gene families.
    • Work has involved (and continues to involve) structure changes, new isoforms, and re-classification of CDSs as pseusogenes
  • Review of some CDSs models based on lincRNA data from David Greenstein (U. Minnesota)
  • Comprehensive re-annotation of hlb-1 locus (based on feedback from a researcher from Penn state university)

Development

  • New infrastructure for curating RNASeq meta data
    • Ini file under version control, maintained by a combination of scripts and manual curation
    • Will be a input to a script that generates the Track Hub (labelling tracks correctly etc)
  • Continued work on using Trinity to "distill" RNASeq data for use in UTR addition to coding models

ParaSite

  • Release 5 due soon
    • BioMart currently being build
    • Full testing will be done early next week
      • Focus on C. elegans, and two new assemblies (E. multicularis and H. microstoma)
  • Starting to look into Biomart alternatives (elastic search)
  • ParaSite talk at the EG SAB
  • Lots of work on documentation
  • ParaSite expresso - conversations with Caltech about setting this up


January 05, 2016

In attendance: KH, PD, GW, MP

Curation

  • C. elegans
    • ncRNAS
      • Looked into classification in WormMine. Need to liaise with OICR to make sure right tag(s) being used as primary biotype
      • tRNAs
        • HelpDesk ticket on absence GGG (Proline)-antocodon tRNA in C. elegans. This is known (and true for many species).
        • Discussion with Todd Lowe on project to re-name tRNAs across human, fly to make consistent. Should worm be included.
    • RNASeq introns
      • Separation of RNASeq introns by score (<1000 reads, >1000 reads), making it easier to see "high confidence" introns in Fmap
    • Continued curation of genes with CGC names
  • B. malayi
    • Remapping of TIGR models to new V4 assembly. Should help with gene name mapping
    • Amendments to life-stage ontology
    • New RNASeq libraries curated and aligned, ready for WS253
    • Continue to chase why V3 assembly STILL not correct in ENA/NCBI

Development / Production

  • Trinity pipeline
    • Comparison of results using different input data sets
  • QC checks in build
    • Calculation of statistics at key checkpoints in the build
      • This is already in place, but we should make it more robust
  • Assembly Hub
    • WS252 hub built. New Brugia assembly seems to have been handled correctly
  • Ensembl Genomes 31
    • We need to do compara production for this (next week)

General

  • Started preparation of SAB talks