Ensembl QA

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Revision as of 00:17, 16 December 2010 by Marygoldman (talk | contribs) (adding bit about watchin for blast tabs)
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There are periodic updates to all Ensembl Genes tracks in all dbs. Here is a list of things to do in addition to the regular QA you would do normally for a track:

  • Run qaEnsGenes.csh
    • Run it before you push to beta, as it compares dev to beta. You'll lose that comparison if you push too soon.
  • All Ensembl builds are documented in the single file:
   src/hg/makeDb/doc/makeEnsembl.txt
  • You can find all ensembl gene builds in:
   /hive/data/genomes/<db>/bed/ensGene.NN/
where NN is the ensembl version number.
  • To get the links to go to the correct place at Ensembl, you will have to check for the appropriate rows in trackVersion table in hgFixed database
    • Basically, lines from trackVersion need to be copied over into the hgFixed database on beta and the RR. Do this as you push the tables along.
    • You can also manipulate the dates so the current version says 'current'. However, that does not seem to be a rule.
  • New: You also need to update the blastTabs if the zebrafish assembly used in hgGene got new Ensembl Genes. Talk to Brooke or Mary if this is case.