Thank you very much that helped me come up with a solution. Leif
On Thu, 21 Apr 2011 12:21:41 -0700, Pauline Fujita <[email protected]> wrote: > 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
