You are correct Alper, the wigEncode will distort your data when large values are next to small values. See also:
http://genomewiki.ucsc.edu/index.php/Wiggle If you switch to the graphing format bigWig you can avoid this situation. See also: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format --Hiram Alper Kucukural wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
