Hi Marius, I forgot to mention that the density data generated by importing a track into Genome Graphs are available in the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) via the "group: Custom Tracks" menu. You can download the data by selecting "region: genome" and entering a name for the file in the "output file" box.
-- Brooke Rhead UCSC Genome Bioinformatics Group On 05/09/11 11:17, Brooke Rhead wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
