[Gmod-help] GBrowse Quantitative data upload
Dave Clements, GMOD Help Desk
gmodhelp at googlemail.com
Thu Aug 20 19:18:48 EDT 2009
Hi Tripti,
On Tue, Aug 18, 2009 at 4:14 AM, Tripti Grover<tripti.grover at gmail.com> wrote:
> Hi
> Thanks Dave for your reply.
>
> I have uploaded Quantitative data for three experiments on my Mac OS X by
> creating their wig files and then uploading the respective gff3 files
> created after running the wiggle2gff3 script. Using the glyph wiggle_density
> i can observe transcriptional profiles for all three experiments viz
> seedling, root, young leaf (YL) as separate tracks but they are all grouped
> under one checkbox heading "Transcriptional Profile". I need separate
> checkbox for each experiment so that the user can turn a track on or off as
> desired.
>
>
>
> For this i created separate track configuration stanzas like [Transchip 1],
> [Transchip 2], ...etc in the conf file as shown below ,but,found it of no
> use as, checking one box shows expression profile for all three
> experiments. Like if root is checked it shows data about all stages
> seedling, root as well as young leaf.
>
> [TransChip1]
>
> feature = microarray_oligo
>
> glyph = wiggle_density
>
> height = 30
>
> bgcolor = blue
>
> category = Genes
>
> description = 1
>
> key = Seedling
>
> [TransChip2]
>
> feature = microarray_oligo
>
> glyph = wiggle_density
>
> height = 30
>
> bgcolor = blue
>
> category = Genes
>
> description = 1
>
> key = Root
>
> [TransChip3]
>
> feature = microarray_oligo
>
> glyph = wiggle_density
>
> height = 30
>
> bgcolor = blue
>
> category = Genes
>
> description = 1
>
> key = Young Leaf
See my previous email for an explanation of what is going on here.
The "feature" is what determines what is displayed in the track. The
"key" just determines the label the track is given, not what is shown
in it.
> Secondly, clicking the wiggle density glyph at a particular position should
> display the corresponding score which is not getting displayed. It displays
> exactly same information at all positions, even the length and position
> values displayed are always the same.I have attached 2 screen shots for both
> my problems.
This is the only behavior I have ever seen for wiggle tracks. The
behavoir you want would be a nice addition. I have no idea if this is
possible, or how much effort it would be.
In the future, for GBrowse questions, I encourage you to submit the
questions to the GBrowse mailing list. That way you will get over 100
people looking at your question.
Thanks,
Dave C.
> Kindly suggest the modifications i need to make so that only the desired
> track is displayed and score details can also be viewed . The data has to be
> uploaded using a wig file, and i have around 20 experiments to be displayed.
>
> Thanking You
>
> Regards
>
> Tripti
> On Thu, Aug 13, 2009 at 12:39 PM, Dave Clements, GMOD Help Desk
> <gmodhelp at googlemail.com> wrote:
>>
>> 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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>
>
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