Hi Vanessa,
Thanks for your help. It is working now. Perhaps it may be useful for other users, the bigDataUrl should be on the same line while the other urls should be on new lines. Cheers, Zen ******************************************* The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. > -----Original Message----- > From: Vanessa Kirkup Swing [mailto:[email protected]] > Sent: 29 September 2011 21:25 > To: LU Zen > Cc: [email protected] > Subject: Re: [Genome] URL for multiple custom tracks > > Hi Zen, > > One of our developers also suggests putting a trackline before each > url in the tracks.txt, something like this: > > track name=myPsl > > ftp://ftp.ed.ac.uk/edupload/btRosa26_sense_EST_noTC_blat_Btau4.psl > > track name=myBam type=bam > bigDataUrl=ftp://ftp.ed.ac.uk/edupload/Boran_Rosa26_loci.bam > > track name=myLoci > > ftp://ftp.ed.ac.uk/edupload/btRosa26_locus_dbSNP.bed > > track name=myUnfilteredLoci > > ftp://ftp.ed.ac.uk/edupload/Boran_Rosa26_loci_unfiltered.bed > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: Vanessa Kirkup Swing <[email protected]> > Date: Thu, Sep 29, 2011 at 12:46 PM > Subject: Re: [Genome] URL for multiple custom tracks > To: LU Zen <[email protected]> > Cc: "[email protected]" <[email protected]> > > > Hi Zen, > > It looks like there are a couple of things that you need to take a look at: > > 1) The file that contains your URLs > (ftp://ftp.ed.ac.uk/edupload/all_tracks.txt) doesn't exist. > > > 2) One of your custom tracks is a BAM file and not a BED file. Please > take a look at the information on BAM format: > > http://genome.ucsc.edu/goldenPath/help/bam.html > > Please note that your BAM track will need to have a "track" line with > a "bigDataUrl" specified that points to the BAM file. > > > Hope this helps solves your issues. Please contact the mailing list if > you have further questions. > > Vanessa Kirkup Swing > UCSC Bioinformatics Group > > > > > ---------- Forwarded message ---------- > From: LU Zen <[email protected]> > Date: Thu, Sep 29, 2011 at 12:00 PM > Subject: Re: [Genome] URL for multiple custom tracks > To: "[email protected]" <[email protected]> > > > Hi Vanessa, > > I just created a text file with the following urls: > ftp://ftp.ed.ac.uk/edupload/btRosa26_sense_EST_noTC_blat_Btau4.psl > ftp://ftp.ed.ac.uk/edupload/Boran_Rosa26_loci.bam > ftp://ftp.ed.ac.uk/edupload/btRosa26_locus_dbSNP.bed > ftp://ftp.ed.ac.uk/edupload/Boran_Rosa26_loci_unfiltered.bed > > and then used this > http://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau4&position=chr22:17680195- > 17691402&hgt.customText=ftp://ftp.ed.ac.uk/edupload/all_tracks.txt. > But nothing got loaded. > > Cheers, > Zen > > ******************************************** > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > Disclaimer: This e-mail and any attachments are confidential and > intended solely for the use of the recipient(s) to whom they are > addressed. If you have received it in error, please destroy all copies > and inform the sender. > > > > -----Original Message----- > > From: Vanessa Kirkup Swing [mailto:[email protected]] > > Sent: 29 September 2011 19:26 > > To: LU Zen > > Cc: [email protected] > > Subject: Re: [Genome] URL for multiple custom tracks > > > > Hi Zen, > > > > You will need to create a single file with all the custom tracks in > > it. This single file can be a list of all the URLS that were > > contained in the link that you sent us and then you will need to point > > to that single file with the hgt.customText=URL format. > > > > Also, you can share custom tracks by using sessions which you can get > > to by clicking on "Session" from the blue navigation bar. There is a > > User's Guide on the Sessions page for more information on how it > > works. > > > > If you have further questions, please contact the mailing list: > > [email protected]. > > > > Vanessa Kirkup Swing > > UCSC Genome Bioinformatics Group > > > > > > ---------- Forwarded message ---------- > > From: LU Zen <[email protected]> > > Date: Thu, Sep 29, 2011 at 10:44 AM > > Subject: [Genome] URL for multiple custom tracks > > To: "[email protected]" <[email protected]> > > > > > > Hi, > > > > I'm trying to share a few custom tracks with some colleagues. When I > > used the following url, it just displays the final track. However, if > > I enter each track separately, they will all appear in the final > > output. Perhaps I have not entered the url correctly or is it just no > > possible to have multiple tracks in the url? This is the url I used: > > http://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau4&position=chr22:17680195- > > > 17691402&hgt.customText=ftp://ftp.ed.ac.uk/edupload/btRosa26_sense_EST_noTC_blat_Btau4.psl&hgt.customTex > > > t=ftp://ftp.ed.ac.uk/edupload/Boran_Rosa26_loci_unfiltered.bed&hgt.customText=ftp://ftp.ed.ac.uk/eduploa > > > d/btRosa26_locus_dbSNP.bed&hgct_customText=track%20type=bam%20bigDataUrl=ftp://ftp.ed.ac.uk/edupload/Bor > > an_Rosa26_loci.bam > > > > Any help is appreciated. > > > > Thanks, > > Zen > > > > ******************************************** > > > > > > The University of Edinburgh is a charitable body, registered in > > Scotland, with registration number SC005336. > > Disclaimer: This e-mail and any attachments are confidential and > > intended solely for the use of the recipient(s) to whom they are > > addressed. If you have received it in error, please destroy all copies > > and inform the sender. > > > > > > The University of Edinburgh is a charitable body, registered in > > Scotland, with registration number SC005336. > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
