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

[Scott Cain]

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