<html>
<body>
Thank you Scott,<br><br>
I trusted the 3rd party .agp -> .gff converter :)<br>
So I will try a conversion of my own, read and follow more closely the
gff3 definitions<br><br>
-- One thing that confuses me is the alternate lines in the .agp
file<br>
<a href="http://www.animalgenome.org:2358/hu/share/scott/chr8.agp">
http://www.animalgenome.org/hu/share/scott/chr8.agp</a> like:<br><br>
<pre>Chr8<x-tab> </x-tab>385914<x-tab>
</x-tab>445952<x-tab> </x-tab>14<x-tab>
</x-tab>W<x-tab>
</x-tab>7180003368659<x-tab>
</x-tab>1<x-tab>
</x-tab>60038<x-tab>
</x-tab>-
Chr8<x-tab> </x-tab>445952<x-tab>
</x-tab>445953<x-tab> </x-tab>15<x-tab>
</x-tab>N<x-tab>
</x-tab>1<x-tab>
</x-tab>fragment<x-tab>
</x-tab>yes
</pre>which I am not sure how to deal with. Any suggestion?<br>
Zhiliang<br><br>
<br>
At 11:42 AM 9/23/2008 -0400, Scott Cain wrote:<br>
<blockquote type=cite class=cite cite="">Hi Zhiliang,<br><br>
There are at least a few problems with your GFF:<br><br>
1. There is no reference sequence line. That is, there is no
line<br>
that tells GBrowse what Chr8 is. You should have a line like
this:<br><br>
Chr8 . chromosome 1
10000000 . . . Sequence
Chr8<br><br>
2. On the gap lines, you have '1' for the strand, but it should be<br>
either + or -.<br><br>
3. Also on the gap lines, you have only one word, 'gap', for the
first<br>
tag value pair; there should be a name after the word 'gap'.<br><br>
I don't know for sure if just these changes will fix your problem;<br>
I'll test it shortly.<br><br>
Scott<br><br>
<br>
On Tue, Sep 23, 2008 at 11:33 AM, Zhiliang Hu <zhu@iastate.edu>
wrote:<br>
> Yes, they are here:<br>
>
<<a href="http://www.animalgenome.org/hu/share/scott/" eudora="autourl">
http://www.animalgenome.org/hu/share/scott/</a>
><a href="http://www.animalgenome.org/hu/share/scott/" eudora="autourl">
http://www.animalgenome.org/hu/share/scott/</a><br>
><br>
> Thanks!<br>
> Zhiliang<br>
><br>
> At 11:21 AM 9/23/2008 -0400, you wrote:<br>
>>Hi Zhiliang,<br>
>><br>
>>Could you please also send a sample of you GFF? I imagine
the problem<br>
>>is a combination of your data and your config.<br>
>><br>
>>Scott<br>
>><br>
>><br>
>>On Tue, Sep 23, 2008 at 11:17 AM, Zhiliang Hu
<zhu@iastate.edu> wrote:<br>
>>> Hi Scott,<br>
>>><br>
>>> 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 ...<br>
>>><br>
>>> Thanks!<br>
>>> Zhiliang<br>
>>><br>
>>><br>
>><br>
>><br>
>><br>
>>--<br>
>>------------------------------------------------------------------------<br>
>>Scott Cain, Ph. D. cain.cshl@gmail.com<br>
>>GMOD Coordinator
(<a href="http://gmod.org/" eudora="autourl">http://gmod.org/</a>)
216-392-3087<br>
>>Cold Spring Harbor Laboratory<br>
><br>
><br><br>
<br><br>
-- <br>
------------------------------------------------------------------------<br>
Scott Cain, Ph. D. cain.cshl@gmail.com<br>
GMOD Coordinator
(<a href="http://gmod.org/" eudora="autourl">http://gmod.org/</a>)
216-392-3087<br>
Cold Spring Harbor Laboratory</blockquote></body>
</html>