Dear Jeniffer, Thank you for your quick response. I think, it is before scaling, because, you can change scaling option in trackDb table or from the web interface, even you change and make it 40 for example, the data is not there. I think, this data is not encoded correctly(or maybe intentionally) into its wib file. Because, the details are in wib files. More interestingly, it is not the deletion on whole peak. The half of the region is deleted and the rest is there. So, there must be something in wigEncode that it deletes the data in the certain vicinity of an huge peak. Is there any solution for it?. If you upload the files that I sent you on sacCer2, the problem can be seen easily. Thanks, Alper
Jennifer Jackson wrote: > 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
