Hello Sean, If I paste your entry:
track type=bigWig name="SL2901" description="test" bigDataUrl=http://maniatis.c2b2.columbia.edu/Noam/SL2901.bw Into the "Paste URLs or data" box in the custom track menu here: http://genome.ucsc.edu/cgi-bin/hgCustom I am able to load your track. The "Optional track documentation" box is meant to be a place to input descriptive text that goes into the description page for your custom track. Note that I had to remove a carriage return between "bigDataUrl=" and the actual url - the loader is sensitive to extra line breaks. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 8/3/11 2:27 PM, Sean O'Keeffe wrote: > Hi, > I'm having difficulty displaying a bigWig custom track from a url on the > browser. > here's what I've done: > > File creation: > bowtie -m 1 -S --best --strata -q -p 8 --un no_align/file.fastq --max > mult_align/file.mult.fastq bowtie/indexes/hg19 file.fastq align/file.sam > samtools view -b -S align/file.sam -o align/file.bam > genomeCoverageBed -bg -ibam align/file.bam -g /genomes/hg19.sizes > > align/file.bedgraph > (final bedgraph has no header/header removed) > wigToBigWig align/file.bedgraph /genomes/hg19.sizes align/file.bw > > Visualisation: > I gave the full url address of the bigwig file > As per http://genome.ucsc.edu/goldenPath/help/bigWig.html example three. > I then, firstly left out the optional documentation which gave the error: > "Error Unrecognized format line 1..." when using "Add Custom Tracks" > I then added the track documentation as given in the example above at point > 7* > *track type=bigWig name="SL2901" description="test" bigDataUrl= > http://maniatis.c2b2.columbia.edu/Noam/SL2901.bw > However this resulted in the following error*: > > Error Optional track documentation appears to be either too large (greater > than 50k) or it starts with a track or browser line. This is usually an > indication that the data has been accidentally put into the documentation > field. Only html documentation is intended for this field. Please correct > and re-submit. > > *The url address is valid and public so should be accessible. > Any help would be great, > > Thanks, > Sean* > * > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
