[Gmod-ajax] Tiling Array data and Gene report Page

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[Gmod-ajax] Tiling Array data and Gene report Page

Swapnil Nagar
Hi,

I am working on the JBROWSE

Can I generate the gene report page (as I can do it on Gbrowse 1 + )?

Second issue is with the Tiling array data, Is there is any way to represent tiling array data or in other words signal strength.

If there is, can I have the JSON file for that.

Regards,

Swapnil Nagar

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Re: [Gmod-ajax] Tiling Array data and Gene report Page

Mitch Skinner
On 5/28/2010 1:51 PM, Swapnil Nagar wrote:
> Can I generate the gene report page (as I can do it on Gbrowse 1 + )?
>    

Currently, all JBrowse can do is either 1) the little popup you get when
you click on a feature, or 2) link to a page provided by something else.

So if you have a GBrowse instance going, then you can use JBrowse to
link to the GBrowse gene page, so that the GBrowse gene page opens when
you click on a gene.  You can specify that link using the "urlTemplate"
setting in the config file (with bin/biodb-to-json.pl), or using the
--urltemplate parameter to bin/flatfile-to-json.pl.

JBrowse by itself doesn't currently generate anything like the GBrowse
gene pages, though.

> Second issue is with the Tiling array data, Is there is any way to represent tiling array data or in other words signal strength.
>    

If you can get the data into the wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

or the bedGraph format:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html

then you can display the data in JBrowse, by running the
bin/wig-to-json.pl program on your wiggle/bedGraph file.

Hope this helps,
Mitch

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