[Gmod-help] sample conf file for contig alignments?

[Scott Cain]

Hi Zhiliang,

Are you referring to the label next to the checkbox to turn the track
on?  That is just descriptive text that you put in the track config to
help users figure out what that track is.  For example you could add
to your track configuration a citation line:

[Contigs]
feature     = MD_scaffold
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = navy
label density = 25
citation      = A mapping of contigs onto the cattle genome golden path
bump density  = 100

and that text will show up in the popup balloon that appears when you
mouse over the word Contig or in the list of tracks when you click on
the word Contig.

Scott

On Tue, Sep 23, 2008 at 12:30 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
> Scott - Many thanks!
>
> Now a link to "Contig" shows up http://www.animalgenome.org/cgi-bin/gbrowse/cattle
> which leads to a page complaining "No additional information available" -- I guess at this point it encountered my .gff format problems.  I will work on that, and let you know where I will be.
>
> Thank you!
>
> Zhiliang
>
> At 12:06 PM 9/23/2008 -0400, you wrote:
>>To get GBrowse to display your gff, I only had to add the reference
>>sequence line and modify your track config.  The Contigs track looks
>>like this:
>>
>>[Contigs]
>>feature     = MD_scaffold
>>glyph       = generic
>>height      = 8
>>bgcolor     = cyan
>>fgcolor     = navy
>>label density = 25
>>bump density  = 100
>>
>>Note that putting ":" in the [...] has a special meaning, so you
>>shouldn't do it randomly. Other things I fixed:
>>
>>1. I added a feature = MD_scaffold so that GBrowse would know what
>>kind of features to display
>>
>>2. Removed one of the glyph= lines (I figured you didn't really want
>>to use the dot glyph).
>>
>>Scott
>>
>>
>>On Tue, Sep 23, 2008 at 11:42 AM, Scott Cain <cain.cshl at gmail.com> wrote:
>>> Hi Zhiliang,
>>>
>>> There are at least a few problems with your GFF:
>>>
>>> 1. There is no reference sequence line.  That is, there is no line
>>> that tells GBrowse what Chr8 is.  You should have a line like this:
>>>
>>> Chr8   .   chromosome  1   10000000  .   .   .   Sequence Chr8
>>>
>>> 2. On the gap lines, you have '1' for the strand, but it should be
>>> either + or -.
>>>
>>> 3. Also on the gap lines, you have only one word, 'gap', for the first
>>> tag value pair; there should be a name after the word 'gap'.
>>>
>>> I don't know for sure if just these changes will fix your problem;
>>> I'll test it shortly.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Sep 23, 2008 at 11:33 AM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>>> Yes, they are here:
>>>> <http://www.animalgenome.org/hu/share/scott/>http://www.animalgenome.org/hu/share/scott/
>>>>
>>>> Thanks!
>>>> Zhiliang
>>>>
>>>> At 11:21 AM 9/23/2008 -0400, you wrote:
>>>>>Hi Zhiliang,
>>>>>
>>>>>Could you please also send a sample of you GFF?  I imagine the problem
>>>>>is a combination of your data and your config.
>>>>>
>>>>>Scott
>>>>>
>>>>>
>>>>>On Tue, Sep 23, 2008 at 11:17 AM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>>>>> Hi Scott,
>>>>>>
>>>>>> The best is if you could trim off all other features and leave me with a bare alignment view only.  Then I can experiment/add other parts back in ...
>>>>>>
>>>>>> Thanks!
>>>>>> Zhiliang
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>--
>>>>>------------------------------------------------------------------------
>>>>>Scott Cain, Ph. D. cain.cshl at gmail.com
>>>>>GMOD Coordinator (http://gmod.org/) 216-392-3087
>>>>>Cold Spring Harbor Laboratory
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D. cain.cshl at gmail.com
>>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>>> Cold Spring Harbor Laboratory
>>>
>>
>>
>>
>>--
>>------------------------------------------------------------------------
>>Scott Cain, Ph. D. cain.cshl at gmail.com
>>GMOD Coordinator (http://gmod.org/) 216-392-3087
>>Cold Spring Harbor Laboratory
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory