Hi Marius, Have you seen the Genome Graphs tool? http://genome.ucsc.edu/cgi-bin/hgGenome (You can also get to it by hitting the "Home" link and then "Genome Graphs" on the left-hand menu.)
To create a density graph for any existing track, hit the "import" button, select the track from the drop-down menus, optionally give it a name, then hit "submit". Once the track has been loaded, you have to select it from the "graph" drop-down menu to see it. For more details, see the User's Guide: http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html > And: How reliable/trustworthy are these data? That depends on which track you are viewing. To read about the data sources and methods used to create any of the tracks in the Genome Browser, go to the main Browser page (http://genome.ucsc.edu/cgi-bin/hgTracks) and either click on the blue track name above the drop-down menus, or click on the gray button directly to the left of a track that is already displayed. > Also, I'd like to know, how I can find the exact position of the > centromeres of the ""non-model"" organism genomes (i.e. stickleback)? This information is not available for all organisms. If it is available, it will be described in the "Gap" track. I hope this information is helpful. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 05/07/11 02:14, [email protected] wrote: > Hello everyone, > > I'd like to create a heat map (gene densities). ENSEMBL offers a graph > for gene densities (they distinguish between "known" and "novel" > genes). However, I contacted the people from ENSEMBL, but apparently > these gene density data cannot be downloaded (neither the graph): > > http://www.ensembl.org/Tetraodon_nigroviridis/Location/Chromosome?r=1:783604-1032531 > > Is there a way to get such a graph or all the info to plot such a > graph oneself from UCSC? Where can I get it? > > And: How reliable/trustworthy are these data? As I've seen in ENSEMBL, > most genes of the ""non-model"" organisms (i.e. Medaka) are > categorized as "novel genes". Are these genes predicted by homology > when compared to other genomes? > > > > Also, I'd like to know, how I can find the exact position of the > centromeres of the ""non-model"" organism genomes (i.e. stickleback)? > > Thank you a lot for your help, > > Marius > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
