Good Afternoon Christelle:
The bigWig files are not designed to be submitted with the customText URL.
They are designed to function
with the bigDataUrl specification in your track definition line.
To use bigWig files, place them on a WEB server so they can be accessed via a
URL. Use that URL in
the bigDataUrl reference in the track definition line. Therefore, your
complete submission for such
a custom track is a single track definition line.
If you want to construct a genome browser URL that will use this track. Place
the one line content
of your track definition line into a file. Place that one-line file on a WEB
server and then use the
URL to that one-line file in your customText URL reference. The genome browser
will pick up your
one line track definition to define the track from the customText URL, and then
it will use the bigDataUrl in that
track definition line to access the bigWig data.
You also have the alternative of hosting your tracks in a data hub:
http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
--Hiram
ROBERT Christelle wrote:
> Dear UCSC genome browser team,
>
> I would like to display custom ChIP-seq tracks stored as bigWig format. The
> tracks display successfully when I use a custom track configuration file
> stored on a live server (cf. test.txt file) – please see example below:
> http://genome.ucsc.edu/cgi-bin/hgTracks?org=mm9&position=chr18%3A61265226-61290793&hgt.customText=http://www.macrophages.com/testtracks/test.txt
>
> Now, if I generate the file through a web application and provide the file as
> an Input stream to the “hgt.customText” parameter in the UCSC custom track
> URL (please see full URL below), I receive the following error:
> # -- Error:
> Unrecognized format line 3 of
> http://www.macrophages.com/BIW-2/DisplayUCSCTrack.action?chromosome=chr18:
> (note: chrom names are case sensitive)
> # -- URL:
> http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr18%3A61265226-61290793&hgt.customText=http://www.macrophages.com%2FBIW-2%2FDisplayUCSCTrack.action%3Fchromosom%3D18%26amp%3Bassembly%3Dmm9%26amp%3Bstart%3D61265226%26amp%3Bend%3D61290793
>
> The file generated by the web application has the same content as that stored
> at: http://www.macrophages.com/testtracks/test.txt, which displays all custom
> tracks as desired (as mentioned above).
>
> Would you have any idea as to why there is a reported error on line 3 when
> the content of the file doesn’t seem to be an issue (as tested with parameter
> hgt.customText equal to http://www.macrophages.com/testtracks/test.txt)?
>
> Thank you very much for your help.
>
> Christelle
> --
> Christelle Robert, PhD
>
> Research Fellow
> The Roslin Institute & R(D)SVS
> University of Edinburgh
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