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

[Zhiliang Hu]

Scott  - Thank you for your attention to the details!

I will take a note on it.

Appreciate it!

Zhiliang


At 12:41 PM 9/23/2008 -0400, Scott Cain wrote:
>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