User generated custom tracks: Difference between revisions
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Tracks providing CpG island strength predictions and mapping of bona fide CpG islands for the human genome (hg17/hg18). The tracks are based on large-scale epigenome predictions, which give rise to an improved and quantitative annotation of CpG islands. Additional information on these tracks is available from the [http://neighborhood.bioinf.mpi-sb.mpg.de/CpG_islands_revisited/ supplementary website] and from the corresponding paper Bock, C. <I>et al.</I> [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030110.eor CpG island mapping by epigenome prediction] to appear in PLoS Comput Biol. For prioritization of candidate regions, the quantitative CpG island strength predictions are recommended (hg17/hg18). For genome annotation, three maps of bona fide CpG islands are provided: (i) a highly specific map (hg17/hg18), (ii) a balanced map <B>recommended for most applications</B> (hg17/hg18) and (iii) a highly sensitive map (hg17/hg18). Finally, all tracks can be viewed simultaneously (hg17/hg18), which | Tracks providing CpG island strength predictions and mapping of bona fide CpG islands for the human genome (hg17/hg18). The tracks are based on large-scale epigenome predictions, which give rise to an improved and quantitative annotation of CpG islands. Additional information on these tracks is available from the [http://neighborhood.bioinf.mpi-sb.mpg.de/CpG_islands_revisited/ supplementary website] and from the corresponding paper Bock, C. <I>et al.</I> [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030110.eor CpG island mapping by epigenome prediction] to appear in PLoS Comput Biol. For prioritization of candidate regions, the quantitative CpG island strength predictions are recommended ([http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&hgt.customText=http://genomewiki.ucsc.edu/images/2/26/Hg17.customText.UCSC_GGM_CombinedEpigeneticScore.txt hg17]/[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/1/1b/Hg18.customText.UCSC_GGM_CombinedEpigeneticScore.txt hg18]). For genome annotation, three maps of bona fide CpG islands are provided: (i) a highly specific map ([http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&hgt.customText=http://genomewiki.ucsc.edu/images/c/c2/Hg17.customText.UCSC_GGM_SpecificCGIs.txt hg17]/[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/2/2c/Hg18.customText.UCSC_GGM_SpecificCGIs.txt hg18]), (ii) a balanced map <B>recommended for most applications</B> ([http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&hgt.customText=http://genomewiki.ucsc.edu/images/f/f4/Hg17.customText.UCSC_GGM_BalancedCGIs.txt hg17]/[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/2/2c/Hg18.customText.UCSC_GGM_BalancedCGIs.txt hg18]) and (iii) a highly sensitive map ([http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&hgt.customText=http://genomewiki.ucsc.edu/images/1/1b/Hg17.customText.UCSC_GGM_SensitiveCGIs.txt hg17]/[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/6/6e/Hg18.customText.UCSC_GGM_SensitiveCGIs.txt hg18]). Finally, all tracks can be viewed simultaneously ([http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&hgt.customText=http://genomewiki.ucsc.edu/images/6/63/Hg17.customText.UCSC_GGM_All.txt hg17]/[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/9/92/Hg18.customText.UCSC_GGM_All.txt hg18]). | ||
==How To Information== | |||
To host custom tracks in the genome wiki, prepare two files to upload to the genome wiki as data files. | |||
One file will be your data in .bb bigBed or .bw bigWig format. | |||
The second file is a simple one-line file which is the <I>track type=bigBed db=<DB></I> line with a <I>bigDataUrl</I> | |||
reference to your .bb bigBed or .bw bigWig data file previously loaded in the genomewiki. | |||
To host multiple tracks in a single reference, add any number of track definition lines in | |||
the second file with <I>bigDataUrl</I> references to all your track data files. | |||
To make a URL reference to the genome browser from a wiki page, with your custom tracks in that genome browser, | |||
use the URL format: | |||
<PRE> | |||
http://genome.ucsc.edu/cgi-bin/hgTracks?db=<DB>&hgt.customText=http://genomewiki.ucsc.edu/images/.../yourTrackLineFile.txt | |||
</PRE> | |||
Indicate the database your tracks apply to in your track line with db=<DB> and in the URL hgTracks reference. | |||
You can find the genomewiki URL reference in the <I>/images/</I> path by looking at the upload results page | |||
of your .bb bigBed or .bw bigWig format file. | |||
Latest revision as of 18:57, 19 March 2010
Testing genomewiki hosting bigBed/bigWig custom tracks
Human assembly custom tracks
Tracks providing CpG island strength predictions and mapping of bona fide CpG islands for the human genome (hg17/hg18). The tracks are based on large-scale epigenome predictions, which give rise to an improved and quantitative annotation of CpG islands. Additional information on these tracks is available from the supplementary website and from the corresponding paper Bock, C. et al. CpG island mapping by epigenome prediction to appear in PLoS Comput Biol. For prioritization of candidate regions, the quantitative CpG island strength predictions are recommended (hg17/hg18). For genome annotation, three maps of bona fide CpG islands are provided: (i) a highly specific map (hg17/hg18), (ii) a balanced map recommended for most applications (hg17/hg18) and (iii) a highly sensitive map (hg17/hg18). Finally, all tracks can be viewed simultaneously (hg17/hg18).
How To Information
To host custom tracks in the genome wiki, prepare two files to upload to the genome wiki as data files.
One file will be your data in .bb bigBed or .bw bigWig format.
The second file is a simple one-line file which is the track type=bigBed db=<DB> line with a bigDataUrl reference to your .bb bigBed or .bw bigWig data file previously loaded in the genomewiki.
To host multiple tracks in a single reference, add any number of track definition lines in the second file with bigDataUrl references to all your track data files.
To make a URL reference to the genome browser from a wiki page, with your custom tracks in that genome browser, use the URL format:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=<DB>&hgt.customText=http://genomewiki.ucsc.edu/images/.../yourTrackLineFile.txt
Indicate the database your tracks apply to in your track line with db=<DB> and in the URL hgTracks reference. You can find the genomewiki URL reference in the /images/ path by looking at the upload results page of your .bb bigBed or .bw bigWig format file.
