Hello Alper, The data display issue is most likely related to scale. If autoScaling is on, then smaller peaks will be reduced, possibly even to a single pixel, making them appear to "disappear". The solution is to control the scale yourself.
Track attributes such as windowingFunction, viewLimits, and autoScaling can be manipulated to alter display. See a complete discussion of these and other attributes here: http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/ You might also consider a different graphing format, such as bedGraph, if the data covers only smaller regions. http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format http://genome.ucsc.edu/goldenPath/help/hgWiggleTrackHelp.html Previous answer that may also be helpful: https://lists.soe.ucsc.edu/pipermail/genome-mirror/2009-June/001306.html https://lists.soe.ucsc.edu/pipermail/genome/2010-January/020935.html Please let us know if you need more assistance, Jen --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/31/10 12:35 PM, Alper Kucukural wrote: > Hello, > First of all, I would like to thank you for all of your efforts to make > an extremely useful tool. > I have a problem in wiggle plot that works on our mirror. I attached two > small files to demonstrate the problem. First file chrV.wig.prep has one > peak and peak height is around 20. The second file has (chrV.wig.prep.2) > has two peaks including the peak in the first file. The distance in the > peak regions is around 800 base. > But here the height of first peak is over 100K and the second region is > only 25. So, when I upload the first file, we see the whole region > without any problem. But, in the second file, there is a problem in the > second peak, it only shows after a part of the peak that is, I guess, > after a certain distance from the first peak. > Why are the small peaks deleted in the vicinity of huge peaks? Is it > possible to show all the data? > > -----I am using the commands below to upload a wig file. > I use wigEncode to make wib file. > wigEncode chrV.wig.prep ex5.wig ex5.wib > And load them to our mirror in to sacCer2 genome. > hgLoadWiggle sacCer2 ex5 ex5.wig > And copy the file into gbdb > cp ex5.wib to /gbdb/sacCer2/wib/. > And add a row to trackDB to show the track. > ---- > Thanks in advance, > Best, > Alper Kucukural > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
