display a bed with track definition line

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display a bed with track definition line

Davide Cittaro
Hi there, 
is there a way to display a bed file to UCSC setting the track name and description automatically? I mean, if the bed file contains only the data tabular data, how can I add "track type=bed name=dataset.name" at display time? I get a generic "User track" instead, that means that I have to rename it every time in the UCSC browser (otherwise it will be overwritten by any other custom track )

d
/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
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Italy

tel.: +39(02)574303007
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Re: display a bed with track definition line

Jen Hillman-Jackson
Hi Davide,

Use the Text Manipulation and Edit Attribute functions to build a
"custom" Custom track for UCSC display.

1 - load a track line (with an optional browser line) into your history
2 - concatenate it with your tab file
3 - convert (label) the data as "bed"
4 - the "display at UCSC" function then interprets the track (& browser)
lines just the same as if you loaded the file directly at UCSC

I created a history for you as an example:
http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/label-ct-for-ucsc-display

The history starts with a bed file from UCSC main. I deconstructed it
down into a plain tab file then built it back up into a CT in bed format
with a track line. I expanded (cloned) some steps for clarity - see the
"Edit Attribute" comments for details about what I did.

Please be sure to let us know if would like more help or find something
unexpected.

Have a nice weekend,

Jen
Galaxy Team

On 8/6/10 1:16 AM, Davide Cittaro wrote:

> Hi there,
> is there a way to display a bed file to UCSC setting the track name and
> description automatically? I mean, if the bed file contains only the
> data tabular data, how can I add "track type=bed name=dataset.name" at
> display time? I get a generic "User track" instead, that means that I
> have to rename it every time in the UCSC browser (otherwise it will be
> overwritten by any other custom track )
>
> d
> /*
> Davide Cittaro
>
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
>
> tel.: +39(02)574303007
> e-mail: [hidden email]
> <mailto:[hidden email]>
> */
>
>
>
>
>
> _______________________________________________
> galaxy-user mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-user

--
Jennifer Jackson
http://usegalaxy.org
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Re: display a bed with track definition line

Davide Cittaro
Hi Jennifer,

On Aug 7, 2010, at 4:58 AM, Jennifer Jackson wrote:

Hi Davide,

Use the Text Manipulation and Edit Attribute functions to build a "custom" Custom track for UCSC display.


Right, I may try to create a workflow for this. Meanwhile I've created a xml display_application trying to override the default bed display.
BTW, I've asked the UCSC team if it will be possible to override track definitions via CGI variables... if the feature request will be accepted, it will be possible for the galaxy bed displayer to add a (say) hgt.trackName=foo in the redirect URL


Thanks!

d
/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/




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