Do not capitalize the attribute "name". -Galt
On 08/15/11 14:31, Sean O'Keeffe wrote: > Apologies! > I should have known that. So to recap my question is: > > I wanted to post multiple url tracks on to the browser. I pasted the lines > below but only one track ever shows up (the last one). > Is there a way to paste more than one track url to the text box? > > Thanks, > Sean. > > track type=bigWig Name=wtTDP43_4weeks description=wtTDP43_4weeks bigDataUrl= > http://maniatis.c2b2.columbia.edu/Helaina/BW/wtTDP43_4weeks_A.bw > track type=bigWig Name=wtTDP43_6weeks description=wtTDP43_6weeks bigDataUrl= > http://maniatis.c2b2.columbia.edu/Helaina/BW/wtTDP43_6weeks_A.bw > track type=bigWig Name=mtTDP43_4weeks description=mtTDP43_4weeks bigDataUrl= > http://maniatis.c2b2.columbia.edu/Helaina/BW/mtTDP43_4weeks_A.bw > track type=bigWig Name=mtTDP43_6weeks description=mtTDP43_6weeks bigDataUrl= > http://maniatis.c2b2.columbia.edu/Helaina/BW/mtTDP43_6weeks_A.bw > > On 15 August 2011 17:03, Pauline Fujita <[email protected]> wrote: > >> Hi again Sean, >> >> Thank you for your question. In order to receive an answer in the timeliest >> manner and for the benefit of all of our users, for whom we try to have the >> most comprehensive archives, we request that you resend your email to >> [email protected]. We appreciate your understanding in this matter. >> >> >> >> Best regards, >> >> Pauline Fujita >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> On 08/15/11 11:48, Sean O'Keeffe wrote: >> >>> Hi Pauline, >>> As a follow up to my previous question, I wanted to post multiple url >>> tracks on to the browser. I pasted the lines below but only one track ever >>> shows up (the last one). >>> Is there a way to paste more than one track url to the text box? >>> >>> Thanks, >>> Sean. >>> >>> track type=bigWig Name=wtTDP43_4weeks description=wtTDP43_4weeks >>> bigDataUrl=http://maniatis.**c2b2.columbia.edu/Helaina/BW/** >>> wtTDP43_4weeks_A.bw<http://maniatis.c2b2.columbia.edu/Helaina/BW/wtTDP43_4weeks_A.bw> >>> track type=bigWig Name=wtTDP43_6weeks description=wtTDP43_6weeks >>> bigDataUrl=http://maniatis.**c2b2.columbia.edu/Helaina/BW/** >>> wtTDP43_6weeks_A.bw<http://maniatis.c2b2.columbia.edu/Helaina/BW/wtTDP43_6weeks_A.bw> >>> track type=bigWig Name=mtTDP43_4weeks description=mtTDP43_4weeks >>> bigDataUrl=http://maniatis.**c2b2.columbia.edu/Helaina/BW/** >>> mtTDP43_4weeks_A.bw<http://maniatis.c2b2.columbia.edu/Helaina/BW/mtTDP43_4weeks_A.bw> >>> track type=bigWig Name=mtTDP43_6weeks description=mtTDP43_6weeks >>> bigDataUrl=http://maniatis.**c2b2.columbia.edu/Helaina/BW/** >>> mtTDP43_6weeks_A.bw<http://maniatis.c2b2.columbia.edu/Helaina/BW/mtTDP43_6weeks_A.bw> >>> >>> On 4 August 2011 09:37, Sean O'Keeffe <[email protected] <mailto: >>> [email protected]**>> wrote: >>> >>> Aha, I wasn't aware of the need for the track info as part of the >>> url. It's not totally clear from the example walk through. >>> All is well now though, thanks. >>> >>> S. >>> >>> >>> On 4 August 2011 02:14, Pauline Fujita <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> Hello Sean, >>> >>> If I paste your entry: >>> >>> >>> track type=bigWig name="SL2901" description="test" >>> bigDataUrl=http://maniatis.__c**2b2.columbia.edu/Noam/SL2901._** >>> _bw <http://c2b2.columbia.edu/Noam/SL2901.__bw> >>> >>> <http://maniatis.c2b2.**columbia.edu/Noam/SL2901.bw<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<http://genome.ucsc.edu/cgi-__bin/hgCustom> >>> >>> <http://genome.ucsc.edu/cgi-**bin/hgCustom<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] >>> <mailto:[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 <http://file.bw> >>> >>> >>> Visualisation: >>> I gave the full url address of the bigwig file >>> As per >>> http://genome.ucsc.edu/__**goldenPath/help/bigWig.html<http://genome.ucsc.edu/__goldenPath/help/bigWig.html> >>> >>> <http://genome.ucsc.edu/**goldenPath/help/bigWig.html<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 >>> >>> <http://maniatis.c2b2.**columbia.edu/Noam/SL2901.bw<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] >>> <mailto:[email protected]> >>> >>> >>> https://lists.soe.ucsc.edu/__**mailman/listinfo/genome<https://lists.soe.ucsc.edu/__mailman/listinfo/genome> >>> >>> <https://lists.soe.ucsc.edu/**mailman/listinfo/genome<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
