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

[Jiantao Yu]

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
>
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