Ensembl QA

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
  • Lines from hgFixed.trackVersion on hgwdev need to be copied over to the hgFixed.trackVersion table on mysqlbeta. Do this when you push the tables. The latest entry should have "current" in the dateReference field and the previous entry needs to have the dateReference field updated to whatever month the last Ensembl release was dated.
  • When you push the track to the RR, the entire hgFixed.trackVersion table can be pushed from mysqlbeta to mysqlrr.

• 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.