Re: [Gmod-ajax] is there any tutorial for build a Jbrowse for display microarray data?

[李道丰 <li...@gm...>]

Hi Mitch,

thank you very much for your response
i use BLAT to map the probe sets to the chromosome,so genrated the .psl file
i also found the wiggle file format is suite for display microarray data
what stoped me is where to start
now i got the .psl file generated by BLAT contains probe set locations in
chromosomes
log2 transformed expression value of each probe set of 3 different time
points
i want to use a MySQL database backend
could you give me some hit tell me step by step operation (also good if not
very detail)
sorry if my quest brings trouble to you

Best Regards.

On Tue, Jul 14, 2009 at 11:54 PM, Mitch Skinner
<mit...@be...>wrote:

>  On 07/13/2009 08:46 PM, 李道丰 wrote:
>
> some settings of Jbrowse is same to Gbrowse by Lincoln Stein?
>
>
> The settings related to setting up a data source for feature data are the
> same.  But beyond that, the JBrowse configuration values are different, and
> the syntax of the config file is different.
>
>  *display microarray probe sets locations on the chorosome*
>
>
> What format is this data in?  So far, we've worked mainly with feature data
> in GFF and BED formats; if you can get your input data into one of those
> formats, then we can definitely help you.
>
>  *display corresponding expression value of each probe set*
>
>
> What format is this data in?  For quantitative data, JBrowse currently
> supports the wiggle file format:
> http://genome.ucsc.edu/goldenPath/help/wiggle.html
>
>  *searchable probe sets*
>
>
> You mean, searchable by ID?  This is controlled by the "autocomplete"
> setting in the config file (for biodb-to-json.pl) or the "autocomplete"
> command-line parameter for flatfile-to-json.pl.
>
>  *clicked probe sets linked to an outer database*
>
>
> This is controlled by the "urltemplate" config file setting or command-line
> parameter.  The Dmel demo config file has an example of this:
> http://jbrowse.org/code/jbrowse-master/docs/examples/config/Dmel.json
>
>  additionlly, in the currentlly version of Jbrowse,click an item would
> popup an window- -
> can i replace that behaviour with others like balloon tips?
>
>
> This is one of the things on our to-do list.  You can do it now if you want
> to modify the javascript code yourself; in js/FeatureTrack.js, in the
> loadSuccess method, there's some code to set a property of the track, called
> onFeatureClick.  Changing that method will change what happens when a user
> clicks on a feature.
>
> Regards,
> Mitch
>



-- 
Daofeng Li,PhD Candidate
China Agricultural University