Dear Hiram, Thanks for the solution. Best, Alper
On Mar 31, 2010, at 6:40 PM, "Hiram Clawson" <[email protected]> wrote: > 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
