[Gmod-help] GBrowse Quantitative data upload

[Tripti Grover]

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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