Great! The provided information is very helpful. Thank you very much Mary.
D. On 8/25/10 8:05 PM, Mary Goldman wrote: > Hi Duke, > > We are now able to reproduce what you describe. The default number of > items to display for bigBed tracks is 250, while bed tracks can > display an unlimited number of items (until the maximum total image > height is reached). You can change the default number of items to > display by adding "maxItems=#" to your track line when you are loading > your custom track, where # is the new default number of items to display. > > Please note that your browser may be unable to load the image if there > are too many items in one location. We still recommend using > bedItemOverlapCount to help users visualize bed files with many items > in them. > > I hope this information is helpful. Please feel free to contact the > mail list again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > On 8/25/10 4:09 PM, Mary Goldman wrote: >> Hi Duke, >> >> We are currently unable to reproduce what you describe. Can you >> please send us a bed file that displays differently as a bigBed file? >> It would ideal if this bed file had data in a just a small chromosome >> range so that it was not so big. >> >> Best, >> Mary >> --------------------- >> Mary Goldman >> UCSC Bioinformatics Group >> >> On 8/19/10 8:37 AM, Duke wrote: >>> Hi Hiram, >>> >>> On 8/19/10 11:24 AM, Hiram Clawson wrote: >>>> Good Morning Duke: >>>> >>>> Your track has too many items in the location of view to display them. >>>> The genome browser lowers its visibility until it fits comfortably. >>>> In the worst case, it will only display in 'dense'. >>> So why the bed file acts normally, but the bigBed does not? I think >>> bigBed is a compressed version of bed, so it should act the same as >>> bed. >>> >>> Thanks, >>> >>> D. >>> >>>> You can make a density graph of your track with the kent src utility: >>>> bedItemOverlapCount >>>> in: src/hg/bedItemOverlapCount/ to get an idea of the pile ups. >>>> >>>> --Hiram >>>> >>>> ----- Original Message ----- >>>> From: "Duke"<[email protected]> >>>> To: [email protected] >>>> Sent: Thursday, August 19, 2010 8:16:44 AM GMT -08:00 US/Canada >>>> Pacific >>>> Subject: Re: [Genome] bigBed always be pack >>>> >>>> On 8/19/10 9:56 AM, Duke wrote: >>>>> Hi all, >>>>> >>>>> I tried to convert a bed file to bigbed, and visualized it on our >>>>> local >>>>> UCSC mirror, but unfortunately no matter how I change the setting, >>>>> the >>>>> track always stayed at pack. It seems that full or squish does not do >>>>> anything with the track. Since the track and the file are in our >>>>> local >>>>> server, I can not post link here at the moment, but I will consider >>>>> loading to external host if needed. The bigBedInfo command shows: >>>>> >>>>> $ bigBedInfo adipose-uni.bowtie.bb >>>>> version: 4 >>>>> isCompressed: yes >>>>> isSwapped: 0 >>>>> itemCount: 19,132,866 >>>>> primaryDataSize: 148,503,559 >>>>> primaryIndexSize: 1,208,984 >>>>> zoomLevels: 10 >>>>> chromCount: 25 >>>>> basesCovered: 49,603,138 >>>>> meanDepth (of bases covered): 12.343004 >>>>> minDepth: 1.000000 >>>>> maxDepth: 183964.000000 >>>>> std of depth: 257.659587 >>>>> >>>>> so I think there is nothing wrong with it. Do I have to do something >>>>> else, or did I do something wrong? >>>> Sorry, it should not be "always". Actually if I set the bigBed to >>>> /full/, it is only be /full/ in some range and/or locations. Most of >>>> other cases, it stays at /pack/ visibility. The corresponding bed file >>>> acts correctly (meaning /full/ is /full/ :D). Is this expected or >>>> there >>>> is an option that I have missed? >>>> >>>> Thanks, >>>> >>>> D. >>>> >>>> _______________________________________________ >>>> 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
