Hello Jane, The UCSC Browser does not contain the information needed to anchor the scaffolds to chromosomes. The best suggestion is to contact the assembly authors and ask for help.
The complete credits are on the gateway page, but here is a direct link: http://www.broadinstitute.org/science/projects/mammals-models/guinea-pig/guinea-pig Specifically, their contact email is: [email protected] If you are able to obtain additional data, remember that you can load it back in as a Custom track to view it along with the native UCSC Browser data, as long as the core scaffold coordinates are consistent. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Best wishes for your research project, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/14/10 1:06 PM, Jane Joanna Pappas wrote: > Hello, > > I am currently using the Guinea pig (Cavia porcellus) genome browser > http://genome.ucsc.edu/cgi-bin/hgGateway?db=cavPor3 to locate various cDNA > sequences and have found at least three pertinent scaffolds (3+, 10+ and > 11-), but scaffolds have not yet been anchored to chromosomes, at least not > in the current assembly to my knowledge. Can you make any recommendations > regarding how I may find out how they relate to each other vis-a-vis > chromosomes? I am guessing that G-banding and FISH may be the only > alternative if chromosomal anchors or in silico devices such as more current > assemblies are not available. Any help in this matter would be of great > assistance. Thank you in advance. > > Sincerely, > > Jane > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
