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Discussion items

pedigree?
TimeItemWhoNotes
 GrainGenesTanerpaper accepted, starting work on JBrowse
 breedbasetriticumbase 

genotype data- need loading script for over 90MB of data
- should I create a protocol for each project, I want to download genotype data by project.
use protocol or file for comparison, vcf tools stats 

  • need to subset files over 90MB, Lucas is working on new loading script
  • each experiment should have separate protocol and project (required for download and analysis)
  • need a method to check/QC loaded genotype data (vcf-stats from VCFtools?) 

download page - error loading page "breeders/download"
- /ajax/html/select/genotyping_protocols (not found)
maps data - slow loading large files 

map viewer - added Comparative Map Viewer, slow working with large maps 

 T3 Oat cropontology.org
how to add entries?
 T3  gene annotationClayOat crop ontology
Gene Annotation -
  • using BioMart v43
  • added InterPro description
Uniform marker names 
  • Gene ontology is limited because many UniProt links are deleted, this should be fixed in next release 
  T3 markers ClayUniform marker names
t3 marker 168K 
  T3 BLAST Clayweb blast temporary files filling hard drive, now old files removed daily 

Action items

  •  Clayton L Birkett - memory upgrade for tcapg machine
  •  send the logo to GrainGenes and Lucas
  •  Clayton L Birkett work with Mirella for getting BrAPI  for large datasets