Hi Sergei, The different shades you see at the top are the "whiskers". To turn that of, go to the track controls (click on the title of the track above the display setting pulldown) and where you see "Windowing function", set it to just "mean". For details, click on the "Graph configuration help" link on the track settings page.
So, the overlapping coords are not causing the color issue, however, they are an issue. You should not have overlapping coords. For your last question, in the track controls you have "Data view scaling" set to "auto-scale". Since the lowest values in you blue and red tracks is 0, 0 shows for those tracks. The 'black' track's lowest data point is 1, so that track uses 1. You can manually change this setting in the track controls by changing "Data view scaling" and "Vertical viewing range" settings. If you have any additional questions, please reply to: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 5/27/12 11:32 PM, Sergei Manakov wrote: > Hello, > > I noticed that when I create bedGraph tracks, there are several deferent > shades to the color that I specify in the header with "color" flag. I can't > find info on why such things appear (I think automatically in my case) and > how to interpret it. > > Here is an example session: > > http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Siarheimanakov&hgS_otherUserSessionName=bedgraph_windower > > You can see that the color of blue and red tracks take different shades > near the top of the graphs. > > Here is the top of one of the bedGraph file that does it: > > track type=bedGraph name=chr17_5P_Evelyn.w1000s200.mean.bedgraph > color=0,0,255 maxHeightPixels=100:100:11 visibility=full > chr17 27425305 27426305 0.05 > chr17 27425505 27426505 0 > chr17 27425705 27426705 0 > chr17 27425905 27426905 0.05 > chr17 27426105 27427105 0.05 > chr17 27426305 27427305 0.05 > chr17 27426505 27427505 0.05 > chr17 27426705 27427705 0.092 > chr17 27426905 27427905 0.15 > > > Coordinates are overlapping, maybe that has something to do with different > shades? If so, what would it mean? > > And, finally, one more question -- what determines the lower value in the > display of a bedTrack? In the example in this e-mail you can see that the > black track starts at 1 while all red and blue tracks start at 0. > > thanks very much, > Sergei > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
