Hi Craig, The problem is likely the order of the browser lines. I corrected this by moving "browser hide all" to the top of the stack of browser settings (you had it at the bottom).
I changed this: browser position chr2:222141245-222149245 browser full refGene browser dense snp128 browser pack multiz28way browser dense ruler browser hide all To be this: browser position chr2:222141245-222149245 browser hide all browser full refGene browser dense snp128 browser pack multiz28way browser dense ruler I noticed that some links from your web site are not working (the "zoom out" links), but I am assuming this page is a work in progress. I also noticed that you are opting to put some of the browser attributes in the url and some in the bed file. While some should be in the url (for example, db=hg18), others could be moved out of the url and into the bed file (add line: browser complement_hg18) or even omitted entirely from the url or bed file (org=human position=chr2 - both are redundant with other settings). You may be trying to keep the file as generic as possible so that you can use it for both the zoom-in and zoom-out display. If that is so, then moving the "browser position=XXX" from the bed file to the url will allow you to set the position there depending on the zoom level. Naming the files as .txt seems to not cause any problems, but it might be better to name them with a .bed if you are sharing the data, to avoid confusion about the data type. Please let us know if this addresses the problem or if you need more help, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Craig C Benson" <[email protected]> wrote: > From: "Craig C Benson" <[email protected]> > To: [email protected] > Sent: Friday, February 5, 2010 3:45:07 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Custom track browser line display problem > > Hello, > > We have created a number of hyperlinks from our website at > http://www.urmc.rochester.edu/cvri/research/miano-lab/CArGome.cfm > to display custom tracks in BED format, but are having problems with > the browser lines commands. > > Clicking on the following link directly > http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr2&db=hg18&complement_hg18=1&hgt.customText=http://www.urmc.rochester.edu/cvri/research/miano-lab/documents/EPHA4_ZOUT_UCSC.txt > > results in displaying our custom track, but ignoring the commands for > the browser lines. > > However, if I download the BED-formatted custom track, located here > http://www.urmc.rochester.edu/cvri/research/miano-lab/documents/EPHA4_ZOUT_UCSC.txt > and copy and paste the text into a custom track at the UCSC Genome > browser website, the browser line commands are implemented. > > Has anybody seen this discrepancy? Is there something wrong with my > BED formatted custom tracks? > > Best, > Craig > > > Craig C. Benson, MD > Med-Peds Resident, PGY-3 > University of Rochester Medical Center > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
