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

[Scott Cain]

Hi Zhiliang,

I don't know what agp is, so no, I don't have any suggestions.  Asking
on the GBrowse mailing list for suggestions on converting agp to gff
would be a good idea.  Perhaps BioPerl can do it?

Scott


On Tue, Sep 23, 2008 at 11:55 AM, Zhiliang Hu <zhu at iastate.edu> wrote:
> Thank you Scott,
>
> I trusted the 3rd party .agp -> .gff converter :)
> So I will try a conversion of my own, read and follow more closely the gff3
> definitions
>
> -- One thing that confuses me is the alternate lines in the .agp file
> http://www.animalgenome.org/hu/share/scott/chr8.agp like:
>
> Chr8    385914
>   445952  14
>       W
>        7180003368659
>    1
>        60038
>    -
> Chr8    445952
>   445953  15
>       N
>        1
>        fragment
>         yes
>
> which I am not sure how to deal with.  Any suggestion?
> Zhiliang
>
>
> At 11:42 AM 9/23/2008 -0400, Scott Cain 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