Hello, I do not see a problem with the data. If I zoom in enough and change the view to squish, the display is fine. If I zoom out, the only display option becomes dense. This is the expected behavior.
The threshold for the viewing options can be seen by comparing these two positions below. Load the data and go to the browser (I used hg18 - you did not specify a genome, but it really doesn't matter for this test as long as the chromosome ranges exist). For the initial position, set the view to squish. Maybe toggle between all options to see the changes. Then go back to squish and zoom out 1.5x. The switch to dense for this size of a viewing range is automatic and expected. chr19:52,338,669-52,339,040 chr19:52,338,576-52,339,133 (dense is only view option) You might consider adding in more information (increasing to a BED 5 and adding in a score to add a viewable value to the data that will show in dense) if there is some variability associated with the data. Otherwise, it is all just a black bar at the longer genomic ranges. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Yongsheng Bai" <[email protected]> wrote: > From: "Yongsheng Bai" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Wednesday, December 2, 2009 3:09:23 PM GMT -08:00 US/Canada Pacific > Subject: RE: [Genome] Question > > Hi Jen, > > The short number of lines work well. Please help check attached > file... > > Thanks!!! > > > -----Original Message----- > From: Jennifer Jackson [mailto:[email protected]] > Sent: Wednesday, December 02, 2009 5:20 PM > To: [email protected] > Cc: [email protected] > Subject: Re: [Genome] Question > > Hello, > > Attachments are filtered by the mail program. Maybe you can paste the > first > few lines (maybe 20) from your track into an email, unless it is a > compressed file. If compressed, please create a small version that > still > presents the error and send as an attachment. Make sure to also send > all the > settings you are using on the Custom track page so that I can > duplicate your > steps. You should send the data directly to me. > > My first guess, without seeing the data, is that it may be that the > track > type you are using is not designed to display in squish mode, but I > can > double check for this and other potential problems. > > Thanks, > Jen > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Yongsheng Bai" <[email protected]> wrote: > > > From: "Yongsheng Bai" <[email protected]> > > To: [email protected] > > Sent: Wednesday, December 2, 2009 1:30:10 PM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] Question > > > > Hello, > > > > > > > > Somehow I can't display the stacks for attached file in squish mode > > under > > your user custom track. Could you please let me know why? > > > > > > > > Thanks, > > > > YB > > > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
