[Gmod-help] Can I ask a question of Gbrowse2?

[Scott Cain]

Hi Jiantao,

"subject" should work for your data.  Did you try panning or zooming
to another location to make sure GBrowse wasn't using a cached image
(just reloading isn't enough)?

Scott


On Tue, Apr 24, 2012 at 11:44 AM, Jiantao Yu <joelyu.2003 at googlemail.com> wrote:
> Hi Scott,
>
> Really thanks for you quick reply. I tried to change group-on in the config
> file into
> group_on = display_name                    or
> group_on =subject
>
> However, it seems no effect. I have attached the .gff3 and .conf files, and
> the configure script for the .gff3 data starts at the line of No.1365.
>
> Could you please have a look at them? Thanks very much.
>
> Best regards
> Jiantao
>
>
> 2012/4/24 Scott Cain <scott at scottcain.net>
>>
>> Hello Jiantao,
>>
>> What you are seeing is almost always a result of the config and the
>> data not matching.  I think your "group_on" setting is incorrect; it
>> is usually something like "group_on = display_name" or "group_on =
>> subject".  I don't think setting it equal to the name of the feature
>> type does anything.  If fixing that doesn't work, you could send a
>> sample of the GFF to the list.  Also, there is a section of the
>> tutorial that came with GBrowse that covers xyplots that might help
>> (look for "quantitative data" in the tutorial).
>>
>> Scott
>>
>>
>> On Mon, Apr 23, 2012 at 8:14 PM, Jiantao Yu <joelyu.2003 at googlemail.com>
>> wrote:
>> > Dear Sir/Madam,
>> >
>> > I highly appreciate the smart of GBrowse. When I tried to display the
>> > quantitative data, and set up the zoom with small values, such as 40Kbp,
>> > I
>> > got the picture as is attached (picture1.png). However, I perfer the
>> > blocks
>> > to locate on the same line, rather than being hierarchical. I mean, It
>> > would
>> > be better if the blocks are kept as they are in the zoom of 500Kbp (all
>> > of
>> > the blocks are at one line, shown in the picture2.png). Could you please
>> > tell me how to do this? Many thanks!
>> >
>> > BTW: my configure script is like this:
>> >
>> > [methySW_MSH1_1000K]
>> > feature         = methySW_MSH1_1000K
>> > glyph           = xyplot
>> > graph_type      = boxes
>> > fgcolor         = red
>> > bgcolor         = red
>> > height          = 80
>> > min_score       = 0
>> > max_score       = 1
>> > scale           = none
>> > group_on        = methySW_MSH1_1000K
>> > category        = Quantitative Data
>> > label           = 0
>> > key             = Methylation Profile - MSH1_dr_vs_Col0 (Sliding
>> > Windows:1000K-size)
>> >
>> >
>> > Best wishes,
>> > Jiantao
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research