Dear Nathan, Thank you for your patience. Unfortunately, the links that you sent are no longer working because the custom track can't find the files. I have posted comments below your quoted questions.
"I have crafted a URL from the templates given on the docs page, and the name appears in the 'Custom Tracks' seciton, but not in the image. I just get the description above the track, and nothing on the left hand side." Did you follow the instructions on the following page? http://genome.ucsc.edu/goldenPath/help/bigBed.html Just to be sure do you have the following description field in your track line? description="Image title of your choice" "Also I have previously seen direct links to gzipped wig files e.g." Yes, it is possible to input a URL to a gzipped file. "It happens that this file contains the appropriate header lines, but I'd like try this with a BED file (from and archive) which has no header. Is there a way I can pass the required attributes via the URL?" If the files can be obtained via url, you can give a link to a url that contains the header lines followed by the url of the BED file you are interested in. Hope this helps. If you have further questions, please don't hesitate to contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Nathan Johnson" <[email protected]> To: "Mary Goldman" <[email protected]> Cc: [email protected] Sent: Thursday, October 7, 2010 2:58:59 AM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] Data attachement via URL Hi Mary Thanks for the link. This is very helpful, but I am struggling with one aspect of attaching a bigBed file, namely that I can't get the track name to display in the image. I have crafted a URL from the templates given on the docs page, and the name appears in the 'Custom Tracks' seciton, but not in the image. I just get the description above the track, and nothing on the left hand side. This is the test URL I am using: http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position=chr6:52139181-52142206&hgct_customText=track%20type=bigBed%20name=%22XT67E1_undiff_H3K4me3%2dChIP%2DSeq%22%20description=%22XT67E1_undiff_H3K4me3%22%20visibility=full%20bigDataUrl=http://www.ebi.ac.uk/~njohnson/GSM397402_XT67E1_undiff_H3K4me3%2dChIP%2DSeq.bigbed Also I have previously seen direct links to gzipped wig files e.g. http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&hgt.customText=ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM397nnn/GSM397402/GSM397402_XT67E1_undiff_H3K4me3%2DChIP%2DSeq.wig.gz It happens that this file contains the appropriate header lines, but I'd like try this with a BED file (from and archive) which has no header. Is there a way I can pass the required attributes via the URL? Thanks Nath On 5 Oct 2010, at 19:01, Mary Goldman wrote: > Hi Nathan, > > The documentation here should be able to help you: > http://genome.ucsc.edu/goldenPath/help/customTrack.html#SHARE. > > I hope this information is helpful. Please feel free to contact the mail list > again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > ----- Original Message ----- > From: "Nathan Johnson" <[email protected]> > To: [email protected] > Sent: Tuesday, October 5, 2010 8:40:40 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Data attachement via URL > > Hi > > How would one go about attaching a user data source to the UCSC browser via a > URL? e.g. bed/wig/bam files > > Is this possible? Do you have any documentation defining the syntax required? > > Thanks > > Nathan Johnson > Scientific Programmer > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > Email: [email protected] > TelNo: (+44)1223 492629 > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome Nathan Johnson Scientific Programmer European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Email: [email protected] TelNo: (+44)1223 492629 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
