Hello Sufen, Track's are positioned on the reference genome using coordinates. If a tracks coordinates are outside of the range of the base genome (chromosome, scaffold, etc.), then there is no way to view the data.
A work around is to set up your own mirror, create your own base genome (this could be of any size or sequence content, perhaps only a variant chromosome or other genome region), then once set up either load the annotation data as a custom track or as a native track into your mirror. Loading and maintaining your own genomes in a mirror is certainly possible, but requires hardware and technical resource along with ongoing support to stay current. If this interests you, the kent source tree contains both software and instructions (README docs) for creating a mirror. There is also help in the UCSC FAQ/Help and GenomeWiki documents. The sequence for the alternate genome would need to be obtained from another source. To function properly, there is also a minimum amount of data that needs to be obtained from UCSC (see the document that addresses "Minimum install" in the links below). Starting mirror web help documents: http://genome.ucsc.edu/FAQ/FAQlicense.html http://genomewiki.cse.ucsc.edu/index.php/Category:Mirror_Site_FAQ Joining the mirror mailing list is highly recommended: http://genome.ucsc.edu/contacts.html#mirror https://lists.soe.ucsc.edu/pipermail/genome-mirror/ Thank you! Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/20/10 8:52 AM, Sufen Hu wrote: > Thanks all for your input. > > Is there possible to display some custom detail that out range of the current > assembly? Such as the current size of mouse chr19 is 61,342,430, but based on > our research, the size of mouse chr19 will be 61,352,430 (just for example, > not exactly), can I display the detail track that in the region of 61,342,430 > and 61,352,430? > > Thanks. > > Sufen > ---------- Original Message ---------------------------------- > From: Maximilian Haussler<[email protected]> > Date: Tue, 20 Apr 2010 16:33:02 +0100 > >> Password protection for tracks that are confidential. >> >> Ability to tweak the display of the tracks up to the last detail (some of >> which are not possible with custom tracks, e.g. subtracks, data-matrices, >> etc) >> >> Max >> >> On Tue, Apr 20, 2010 at 4:29 PM, Hiram Clawson<[email protected]> wrote: >> >>> Hosting your own specialty genome assembly that UCSC does not host. >>> Building your own set of tracks that are too large to use in >>> the custom track submission system. >>> >>> --Hiram >>> >>> Sufen Hu wrote: >>>> Hello, >>>> >>>> Just wondering what is the advantage of installing the Genome Browser >>> locally. >>>> >>>> Thanks. >>>> >>>> Sufen >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
