How to set chromAlias for custom genome on local mirror

[Stephen Turner]

Hello. 

We recently set up a local/private mirror (after purchasing an enterprise license). I'm loading a genomes that are either private or aren't in annotation hub. I want to assign aliases to the chromosome names. I have a properly formatted chromAlias.txt file that has the names of the chromosomes present in the fasta in the first column, along with aliases I want to be able to use. How do I get these chromosome aliases to be recognized?

I'm following the directions at https://genomewiki.ucsc.edu/index.php?title=Building_a_new_genome_database to build a new genome. 

I've looked through the mailing list here and the public genome google group messages, and I've looked through the documentation below, and can't seem to find anything.

• Building a new genome database - genomewiki - https://genomewiki.ucsc.edu/index.php?title=Building_a_new_genome_database
• Chrom Alias - genomewiki - https://genomewiki.ucsc.edu/index.php/Chrom_Alias
• Local tracks at mirror sites - genomewiki - https://genomewiki.ucsc.edu/index.php/Local_tracks_at_mirror_sites
• Genome Browser Manual Installation Adding a new, custom (non-UCSC) genome to the browser https://genome.ucsc.edu/goldenPath/help/mirrorManual.html#adding-a-new-custom-non-ucsc-genome-to-the-browser
• UCSC Genome Browser Public Support - Google Groups - https://groups.google.com/a/soe.ucsc.edu/g/genome
  UCSC Genome Browser Mirror-Specific Support - Google Groups - https://groups.google.com/a/soe.ucsc.edu/g/genome-mirror
  

Thanks for pointing me in the right direction!

Stephen

[Gerardo Perez]

Hello, Stephen.

Thank you for using the UCSC Genome Browser and for sending your inquiry.

Could you provide more details on how you formatted your chromAlias.txt file after following the Chrom Alias - genomewiki instructions? And can you share what you see in the Genome Browser when using the formatted chromAlias.txt file? Did you build the genome as a database assembly or as an assembly hub? For database assembly browsers, the chromAlias table needs to be loaded and would be a different type of procedure. Here is an example of loading the chromAlias database table from our makedoc, keep in mind this is more made for internal replication:
https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/xenTro10/initialBuild.txt#L606

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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