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'.
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
