Sergei, Also note that bedGraphToBigWig will indicate that these are illegal files with overlapping coordinates. You might want to use the bigBed format for efficiency and sanity checking: http://genome.ucsc.edu/goldenPath/help/bigBed.html
- Greg On 6/25/12 1:56 PM, Greg Roe wrote: > 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
