Hello Tom, You can add in your own data in relation to an existing genome by creating a custom track. Instructions are located here: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks
To obtain mapping coordinates between genomes, you may need to use Blat first. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign These sections in the help document (above) are relevant for larger scale genomic comparisons * * - Creating a custom annotation track from BLAT output - Using BLAT for large batch jobs or commercial use For your specific example, the squirrel genome itself has a browser already created on our test server. This is development/experimental data that has not gone through QA. http://hgwdev.cse.ucsc.edu/ A final option is to create a local copy of the genome browser and use our tools to build an assembly. http://hgwdev.cse.ucsc.edu/FAQ/FAQlicense Specifically, this section would be of interest to you: http://hgwdev.cse.ucsc.edu/FAQ/FAQlicense#license4 Loading/creating a custom assembly on the UCSC hosted genome browser is not possible. I hope this helps to address your questions, but please let us know if you need additional help. Jennifer Jackson UCSC Genome Bioinformatics Group > In general, I am interested in loading in mammalian genome sequences > not yet in the official UCSC builds. How can I do that? > > Thanks, > > Tom > > > *Tom Marr* > tom.marr at gmail.com > <mailto:genome%40soe.ucsc.edu?Subject=Re:%20%5BGenome%5D%20I%20would%20like%20to%20upload%20the%20sample%20sequence%20of%20the%0A%09Spermophilus%20tridecemliniatus%20%28ground%20squirrel%29%20for%0A%09comparative%20analysis&In-Reply-To=%3C9398883B-3754-4FF0-8F13-8223514DD778%40gmail.com%3E> > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
