Hello Leif, One of our developers had this to say:
This issue is due to the graphing mode "mean+whiskers". At the viewpoint mentioned, two data points from the original data are combined together into a single display bar on the graph. One of the data point values is 6.5376 and the second data point is either 0.1143 or 0.331. Combining either of these small values with 6.5 produces a standard deviation of about 4.3 and a mean of about 3.5. The mean+whiskers graph attempts to show plus or minus one standard deviation from the mean, hence the top of the bar drawn is about 7.8. Changing the graphing mode to simply "mean" will eliminate the standard deviation whiskers. This can be specified on the track line for the custom track with the option windowingFunction=mean Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 04/20/11 13:43, lschjeide wrote: > Hello, > > I am having a y-line location problem with a custom track I have created, > but only at a particular zoom level. > > If you please take a look at the following link, you will see a bar > exceeding the 7.3 y-line mark - which is incorrect. The value is actually > 6.5 or so. But if you zoom in or out from there it is correctly below the > 7.3 y-line. This is using the bigbed format pulling datapoints from our > server here at the institute. > > You will first need to load the tracks: > > http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr6&hgt.customText=http://xgene.molgen.mpg.de/ucsc/pdgenetracks.txt > > Then the specific location and zoom level that has a problem is: > > http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=118&revCmplDisp=0&hgsid=192883729&hgt_doJsCommand=&hgt.out2=+3x+&position=chr6%3A32583705-32592704 > > Thank you in advance for your help with this issue! > > Leif > > > > > On Wed, 29 Sep 2010 20:27:00 +0200, Leif Schjeide > <[email protected]> > wrote: >> Hello, >> >> I have two custom tracks that I would like to display with two other >> listed tracks... >> >> I specify the priority of my custom tracks as 1 and 2, followed by pack >> knownGene and dense gwasCatalog. >> >> All tracks show up - almost as expected. >> >> The problem is that my custom tracks are the third and fourth tracks >> listed instead of the first and second. >> >> I tried playing around with the group field within my custom track >> definition, either setting "user" or "x" or "test" because the notes >> mentioned this had something to do with window positioning of the >> tracks. However the different values had no effect. >> >> In case it makes any difference I have a bigBed type and a bigWig type >> as my two tracks. >> >> I am accessing it as follows: (feel free to test for yourself) >> >> > http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr4&hgt.customText=http://xgene.molgen.mpg.de/ucsc/testbb.txt >> testbb.txt: >> >> track type=bigWig name="P-Value" description=" " visibility=full >> color=50,50,50 altColor=90,90,90 gridDefault=on viewLimits=0.0:20.0 >> yLineMark=7 yLineOnOff=on autoScale=off priority=2 group=user >> bigDataUrl=http://xgene.molgen.mpg.de/ucsc/test.bw >> >> track name="PDGene" type=bigBed description="Parkinson's Disease >> Meta-Analyses Results" color=21,68,6 itemRgb="On" visibility=pack >> priority=1 group=user bigDataUrl=http://xgene.molgen.mpg.de/ucsc/test.bb >> >> browser pack knownGene >> browser dense gwasCatalog >> >> >> >> Thanks in advance for any assistance! >> >> Leif > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
