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changes.mady.by.user Clayton L Birkett

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Date

Location: https://connect.unl.edu/tcapt3/

Attendees

Goals

Discussion items

TimeItemWhoNotes
 

combine genotype experiments

Jean-Luc

This could be done in the select lines by "genotype" page

. Limit combining to same platform (9K, 90K, GBS)

. In cases where lines duplicate, the name can be altered (_duplicate)

Combine

Decided to combine 2 genotype experiments

. (clay)

into 1 experiment then we will not need to change tools

 schedule dates of operating system upgradeClay Birkett, David Hane

install Ubuntu 14.04 on tcap machine. We need to allocate several days when no updates are allowed on production

/backup

machine

schedule over weekend

operating system upgrade scheduled for weekend of Feb 19th

.

 new TCAP hardware? 

plan on adding a new server this summer

 genotype data loading 
  1. merging lines with 50% genotype conflicts (these are not the same line)
  2. Nick/Shiaoman (haplotag) will submit VCF file (Oat)
  3. others? Jeffery (Kevin from MN), Rich (Barley 9K ND)
 harvesting QTLs 
  1. added link for JBrowse, marker, and trial count
  2. added trait description and ontology
  3. added QTLs from imputed genotypes
  4. added grouping by marker and gene
  5. how to combine p values? Do you through out disease trials? Do we need confidence interval for qtl loci?
 problems with DNS and email on T3 machinesClay Birkett, David Hane
  1. email still not delivered to some sites because of USDA limitations

Action items

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