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<div class="moz-cite-prefix">Hi Carson,<br>
<br>
thanks for the clarification. I saw in the code that the Augustus
Widget uses hints, but wasn't sure if and how those were
generated. If they are derived from the evidence alignments,
prefect. That's all I needed anyway. As for the passing of an
external phred_gff, I guess the native Augustus GFF output is a
little wonky - I'll try to convert it to match/match_parts to see
if that helps (but with Maker computing it's own hints, I don't
actually have to...). <br>
<br>
Anyway, thanks again!<br>
<br>
/Marc<br>
</div>
<blockquote
cite="mid:CA+sW3ETtKzitZurwUdLHbMauBwNYp49HOqhK6iY-AY=Oggwgbg@mail.gmail.com"
type="cite">
<div dir="ltr">1) MAKER prefers match/match_part but should be
able to handle any two level feature or even gene/mRNA/exon/CDS
features. Make sure it's infact GFF3 and not GTF or GFF2.
<div><br>
</div>
<div>2) MAKER builds it's own hints based on the evidence
alignments it finds, providing user generated hint files is
not supported. If you already have those, you can just run
augustus directly, since one of the the main benefit of MAKER
is that it finds the hints for you and you would no longer
need that.</div>
<div><br>
</div>
<div>Perhaps you can give more details on what exactly you are
trying to do, and we could help you configure MAKER.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Carson</div>
<div><br>
</div>
</div>
<div class="gmail_extra">
<br>
<br>
<div class="gmail_quote">On Tue, Nov 5, 2013 at 1:55 AM, Marc P.
Hoeppner <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:marc.hoeppner@imbim.uu.se" target="_blank">marc.hoeppner@imbim.uu.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
this is possibly a trivial question, but I am realizing that
Maker does not seem to process augustus files I have
produced externally (augustus 2.7); at least they don't seem
to make it into the final annotation file.<br>
<br>
My question(s) therefore:<br>
<br>
1) What exact GFF features does maker expect for a
'pred_gff' file? Would it happily accept an augustus gff, or
would I need to modify the native augustus features somehow?
(Trying to find out whether this is a Maker issue or some
other problem)<br>
<br>
2) Is there a way to feed hint files to Maker to use with
augustus? Couldn't find anything about that specifically
anyway.<br>
<br>
Regards,<br>
<br>
Marc<br>
<br>
-- <br>
-----------<br>
Marc P. Hoeppner, PhD<br>
Researcher<br>
Department of Medical Biochemistry and Microbiology<br>
Uppsala University, Sweden<br>
<a moz-do-not-send="true"
href="mailto:marc.hoepner@imbim.uu.se" target="_blank">marc.hoepner@imbim.uu.se</a><br>
<br>
<br>
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</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------
Marc P. Hoeppner, PhD
Researcher
Department of Medical Biochemistry and Microbiology
Uppsala University, Sweden
<a class="moz-txt-link-abbreviated" href="mailto:marc.hoepner@imbim.uu.se">marc.hoepner@imbim.uu.se</a></pre>
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