[Gmod-help] GBrowse Quantitative data upload

[Dave Clements, GMOD Help Desk]

Hi Tripti,

First I apologize for the delayed response.  Lincoln's been on
holiday, and Scott and I were at GMOD Europe.  I just got back in the
states yesterday.

And, in case you haven't already got this one figured out, ...

I understand some of what is going on here, but not all of it.  Part
of the problem is that you need a way to distinguish between the two
types of data.  Both the Seedling and Root data have the same source
(GFF3 column 2) and type (column 3) values.  The "feature" clause is
what determines what data is shown in which track.  To get the
different data in different tracks try adding "root" and "seedling" to
the source column. For example:

Chr1 Seedling_Os01g01010 microarray_exp 1903 9817 5.758830 . . Name=Seedling

Then change the track definition to

[TransChip1]
feature        = microarray_exp:Seedling_Os01g01010
...

[TransChip2]
feature        = microarray_exp:Root_Os01g01010
...

I think this will get you the two types of data showing up in the
different tracks.  Also, I don't think "microarray_exp" is an official
SO term.  Is "microarray_oligo" what you want?
http://www.sequenceontology.org/miso/current_cvs/term/SO:0000328

The part I don't understand is why you are not currently seeing both
the seedling and root data in both tracks.

Hope this helps,

Dave C

On Sun, Aug 2, 2009 at 10:34 PM, Tripti Grover<tripti.grover at gmail.com> wrote:
> Dear All,
> We have been trying to upload Quantitative Data for more than one experiment
> to GBrowse locally installed on Mac OS X. In order to do this we've been
> following the Administrative tutorial according to which gff3 file contains
> the data to be displayed.
> Ex :
> Chr1 LOC_Os01g01010 microarray_exp 1903 9817 5.758830 . . Name=Seedling
> Likewise we've appended the above file with the data of another experiment,
> the sample data for which is like :
> Chr1 LOC_Os01g01010 microarray_exp 1903 9817 14.578833 . . Name=Root
> The modifications done in the conf file are as follows :
> [TransChip1]
> feature        = microarray_exp
> glyph          = graded_segments
> graph_type     = boxes
> fgcolor        = red
> bgcolor        = orange
> height         = 10
> min_score      = 0
> max_score      = 15
> category       = Transcriptional Profile
> key            = Seedling
> [TransChip2]
> feature        = microarray_exp
> glyph          = graded_segments
> graph_type     = boxes
> fgcolor        = red
> bgcolor        = orange
> height         = 10
> min_score      = 0
> max_score      = 15
> category       = Transcriptional Profile
> key            = Root
>
> With these data and conf files the display we get in GBrowse is both for
>  Seedling and Root but,the color gradation displayed is the same for both
> even though the scores provided in the gff3 files differ a lot.Probably, the
> data is being displayed from the first data set and not from the other. I am
> also attaching the screen shot of GBrowse interface for the display we are
> getting.
> Kindly suggest what modifications we need to do in Conf and GFF3 files so
> that different data sets can be displayed with corresponding color
> gradations.
> Thanking You
> Regards
> Tripti
> Junior Research Fellow
> Department of Plant Molecular Biology
> University of Delhi
> India



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