Hi Yuan, I think I see what the problem is. The track line needs to be on a separate line from the browser line. Try formatting your data like before (no extra white spaces, hidden letters or hidden returns) except put the browser information on its own line:
browser position chr21:33031597-33041570 track type=bigBed name="test" description="test" visibility=pack itemRgb="On" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/bigBedExample.bb Please note that I took out the extra "browser" before the bigDataUrl since "bigDataUrl" is a track item. I also changed the browser position so that the track opens up to where there is data. For more information about track and browser lines in custom tracks see http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks. I hope this information is helpful. Please feel free to contact the mailing list again if you require further assistance. Best, Mary ----------------------------- Mary Goldman UCSC Bioinformatics Group ----- Original Message ----- From: "Yuan Jian" <[email protected]> To: "Jennifer Jackson" <[email protected]> Cc: [email protected] Sent: Wednesday, May 19, 2010 5:12:49 PM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] Error Missing bigDataUrl setting from track of type=bigBed thanks, I checked the line, there is no hidden letters. here is the sentence. track type=bigBed name="test" description="test" visibility=pack itemRgb="On" browser position chr19:56101420-56105806 browser bigDataUrl=http://genome.ucsc.edu/goldenPath/help/bigBedExample.bb --- On Wed, 19/5/10, Jennifer Jackson <[email protected]> wrote: From: Jennifer Jackson <[email protected]> Subject: Re: [Genome] Error Missing bigDataUrl setting from track of type=bigBed To: "Yuan Jian" <[email protected]> Cc: [email protected] Received: Wednesday, 19 May, 2010, 6:54 PM Update: First of all, apologies for missing the error message in the email subject line! And I think I figured out the problem. The track line is not in one continuous line (the browser line is inserted between track line attributes. Reformat to this and see if it works: browser position chr19:56101420-56105806 track type=bigBed name="xxx" description="xxxx" visibility=pack itemRgb="On" bigDataUrl=http://...../xxxx.bb (note that track line has no hidden returns or newlines in the whitespace in the form). Jennifer On 5/19/10 11:33 AM, Jennifer Jackson wrote: > Hello, > > We are not exactly certain what "error in title" means. Assumption is > that the track was not accepted by the Custom track submission form? > > Some things to check: > > 1) the bigDataUrl can be read outside of you local network ("world" can > see it). > > 2) you followed the procedure exactly as outlined in the help documents > below. Please note the "Troubleshooting" section at the end. Also note > in "Example 3", the third bullet point, where it states that an .as file > is required if itemRgb is being used. Modify the .as file if needed (for > example: if you have a different target assembly). > > http://genome.ucsc.edu/FAQ/FAQformat.html#format1.5 > http://genome.ucsc.edu/goldenPath/help/bigBed.html > > If you are still having problems, please provide more information: > > a) Are you able to follow and load all examples on the bigBed help page? > > b) Send the complete Custom Track entry to me directly (do not post to > the list and I will not post to the list in any replies) and we can > troubleshoot from there. Be sure to note the target assembly and any > other settings you changed from the default on the submission form. Do > not send the .bb file. Also, please paste the error message that you get > from the submission form into your email > > Thanks, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/18/10 5:59 PM, Yuan Jian wrote: >> Hello, >> >> I generated a bb file. but I got error as in title when I post the following >> contents: >> track type=bigBed name="xxx" description="xxxx" visibility=pack itemRgb="On" >> browser position chr19:56101420-56105806 >> bigDataUrl=http://...../xxxx.bb >> >> thanks >> >> >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
