Hi Spencer, Since you are having difficulties converting your bed files into bigBed, this indicates there are problems with your bed files. What kinds of errors are you seeing when you run the bedToBigBed program? Please send your reply to [email protected].
--- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 6/22/2012 11:14 AM, Mahaffey, Spencer wrote: > Hi, > > I'm trying to setup a link that includes multiple custom tracks. To do this > I create a file containing the browser and track lines and link to that. > This part works one track is in a bigBed format and it displays correctly. > The next track is in a gtf or bed format and it does not. I can't figure > out a track line to use a gtf or bed file. The examples in the user guide > for these file types only seem to work if you create a link with one custom > annotation file in the .bed or .gtf formats. I've tried a number of > annotation names to try and get it to read a .bed or gtf file. I'm not sure > if this is possible. It would help me narrow down the problem if anyone > could tell me what the correct track line is to include a .bed or .gtf file > if this is even possible. Since it isn't a format that works with the > bigDataUrl attribute. > > A simple solution that I've tried is converting to bigBed, but I keep running > into problems trying to convert the bed file to a bigBed file so maybe the > problem is in the file and not in trying to include a gtf or bed file this > way, but I can upload the file directly and it works correctly or I can use > the example(below) from the users guide with both the gtf or bed file. > > http://genome.ucsc.edu/cgi-bin/hgTracks?org=rat&position=chr19&; > hgt.customText=http://server/ucsc/transcripts.allSamples.3s.bed > > > > A general example of the annotation file follows: > > browser hide all > browser full ensGene knownGene refGene > track db=rn4 type=bigBed name="AffyRatProbesets" description="Affy Rat Exon > Probesets: Red=Core Green=Full Blue=Extended" visibility=3 itemRgb=On > bigDataUrl=http://username:password@server/ucsc/ratBigBed.bb > track db=rn4 name="RNA Assembled Isoforms" description="Isoforms Constructed > From RNA Seq" visibility=2 > bigDataUrl=http://username:password@server/ucsc/transcripts.allSamples.3s.bed > > Obviously the files for the second track aren't appropriate for bigDataUrl, > but I can't seem to find any documentation about what the attribute name > should be for a bed or gtf file or if something like this is possible as it > seems for this to work the files should be in a bigBed or other documented > format. > > Any suggestions would be greatly appreciated. > > Thank you, > Spencer Mahaffey > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
