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
