Hinxton 2016.01- Meeting minutes

January 08, 2016

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

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)

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

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

In attendance: KH, PD, GW, MP

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

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)