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
