HI Dong,
Please keep responses on the list. That way others can contribute and learn.
You are trying to do something that I did not know could be done, which is trying to add/modify features in an existing track by uploading annotation from the user interface. I was only aware that you could define new tracks this way. Are you trying to modify an existing track, or create a new one?
Also, as far as I know, the uploaded files have to be valid GFF, and the uploaded file is not. Some example lines from the file are:
reference=scaffold_v2_77741
transcript let7_pre 14834-14935
reference=scaffold_v2_4906
transcript mir1_pre 262914-263010
reference=scaffold_v2_15487
transcript mir7_pre 7891-7987
See
http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#upload for more on formatting upload files.
Does that help?
Thanks,
Dave C.
On Tue, Oct 20, 2009 at 2:10 PM,
<donghe@...> wrote:
Hi Dave,
my version is 1.68,
what is stanza definition? I am sending you both configure file and upload
file, and part of gff file.
Thank you
Dong
> Hi Dong,
>
> I've included the GBrowse list in my response. People there my have some
> input as well.
>
> Uploaded data should render the same as native data. Let's get a couple
> of
> obvious questions out of the way first.
>
> What version are you running?
> Can you post your stanza definition from both the GBrowse conf file and
> from
> the uploaded file?
> Can you include a few sample lines of GFF, say enough to define a single
> feature?
>
> Thanks,
>
> Dave C.
>
> On Tue, Oct 20, 2009 at 11:59 AM, <
donghe@...> wrote:
>
>> Hi Dave,
>>
>> I meet a problem on Gbrowse, need your help!
>>
>> The graph on GLEAN:Prediction track is set as transcript glyph( segments
>> connected by line), but when I upload private data into Gbrowse, the
>> graph
>> change to solid bar (see, attached ppt file). Could you tell me what is
>> wrong? and help me fix it ASAP?
>>
>> Thank you very much !
>>
>> Dong
>>
>> ------------------------------------------------------
>>
>> this is the part of config file:
>>
>> [Transcript]
>> feature = transcript:GLEAN3
>> glyph = transcript
>> height = 5
>> fgcolor = blue
>> bgcolor = blue
>> box_subparts = 1
>> key = GLEAN:Prediction
>>
>
>
>
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>
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