Hi Sergei, When drawing a bedGraph there is only one pixel per position to draw. If there are overlaps (more than one data point per position), some data will not/cannot be drawn.
Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 6/18/12 1:11 PM, Sergei Manakov wrote: > 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
