hi Greg, Thanks for your reply. Could you explain in a bit more detail why is it bad to have overlapping intervals in Bedgraph format? I am trying to calculate average coverage in a sliding window, so perhaps Bedgraph is not suitable for this purpose?
thanks, Sergei On 1 June 2012 10:06, Greg Roe <[email protected]> wrote: > 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
