Hello, I am unable to see the complete header (attachments are stripped by the mailing list server).
I do see a few conflicts. First you set as a browser line to "hide all". Then you set a group of tracks to dense. If these tracks are not loaded yet, then there is nothing to set to dense. This is the case for track "a" at least, which you load after the browser line is read. After that, while loading track a, is where you set one of those set as dense to full in the track line (visibility=2). If you want track "a" to be dense, leave it out of the browser line list and set visibility=1 in the track line. If the rest of the tracks are also loaded after the browser line with the list, then the same would apply. Another consideration: you have browser position set to be the entire chr1. All open tracks would default to dense at this zoom level - they cannot be open at full. This may be an artifact of your simplifying the header for the purposes of asking the question. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Hope this helps. If this does not solve the problem, either save the data into a Session and send me a link or send me all of the track/browser lines from your file to start with. Send the exact data, not a simplification (assuming there was one). Include only 10 or so data lines per track, ideally all from the same region of genomic. Send directly to me and do not cc the list so that it will pass through. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Olukemi Abolude" <[email protected]> wrote: > From: "Olukemi Abolude" <[email protected]> > To: [email protected] > Sent: Wednesday, November 11, 2009 8:11:53 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Problems with custom tracks- Browers Line - dense attribute > > My annotation file contains seven tracks (a,b,c,d,e,f,g). All the > tracks are displayed in the genome bowser, but the display mode > defaults to "full" even though I have specified "dense" in the > annotation file. > Please kindly take a look at the first few lines of the file. Am I > doing something wrong? I just need it to default to "dense". > > browser position chr1 > browser hide all > browser dense a b c d e f g > track name=a description="A Points" visibility=2 > ' > ' > ' > > Thanks, > Kemi > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
