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
