Post-Release-Checklist

This page capture the things to remember after the release of UCSC Genes for the new assembly.

wiki pages about known genes

QAing UCSC Genes
UCSC Genes tables
UCSC Genes Staging Process
Post-Release-Checklist

Announce the release

• Make an announcement on the genome-announce mailing list
• Add a news item to the Genome Browser front page
• Tweet the news (Ann usually does this)

Contact various collaborators

Exon Primer Links

For human and mouse, send an email to Tim Strom (http://ihg2.helmholtz-muenchen.de/) so that he knows we are releasing a new UCSC Gene set. He will need to prepare his website for the new UCSC IDs.

HGNC Links to us

For human, contact HGNC: hgnc at genenames dot org to let them know about the update. They will need to rebuild their ucsc2hgnc mappings table.

Galaxy

Galaxy may want to update and/or pre-load these data. Contact Anton at Galaxy (anton at bx.psu.edu) to let him know about the update.

UniProtKB

For all but sacCer and danRer, create a speical file for the folks at UniProt to create their cross-references to us. Run makeUniProtFile.csh on hgwdev. This will create a file an the appropriate downloads directory, e.g.: hgwdev:/usr/local/apache/htdocs-hgdownload/goldenPath/hg19/UCSCGenes/ and then ask for a push of the file to hgdownload.

If any of the download URLs change send an email to uniprot (we usually address these to Benoit Bely) at this address uniprot-prod@ebi.ac.uk. We used to warn uniprot for any new release but have since been informed that this is not necessary if the download urls haven't changed, as their process automatically detects the updates.

The current download URLs are:

ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.cse.ucsc.edu/goldenPath/ce6/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/UCSCGenes/uniProtToUcscGenes.txt

Alert Ensembl

Notify Ensembl that there is a new UCSC Genes set: e-mail to Andy Yates <ayates@ebi.ac.uk> and cc Paul Flicek <flicek@ebi.ac.uk>, Fiona Cunningham <fiona@ebi.ac.uk>, and Javier Herrero <jherrero@ebi.ac.uk>. They use the UCSC Gene IDs in their external reference (xref) tables. Note they also do want to be notified for rn4 even though it is not Known Genes, and they may want to be notified for assemblies with Known-Gene-like gene tracks.