[maker-devel] Maker and external ab-inito predictions

[Marc P. Hoeppner]

Hi Carson,

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...).

Anyway, thanks again!

/Marc
> 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.
>
> 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.
>
> Perhaps you can give more details on what exactly you are trying to 
> do, and we could help you configure MAKER.
>
> Thanks,
> Carson
>
>
>
> On Tue, Nov 5, 2013 at 1:55 AM, Marc P. Hoeppner 
> <marc.hoeppner at imbim.uu.se <mailto:marc.hoeppner at imbim.uu.se>> wrote:
>
>     Hi,
>
>     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.
>
>     My question(s) therefore:
>
>     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)
>
>     2) Is there a way to feed hint files to Maker to use with
>     augustus? Couldn't find anything about that specifically anyway.
>
>     Regards,
>
>     Marc
>
>     -- 
>     -----------
>     Marc P. Hoeppner, PhD
>     Researcher
>     Department of Medical Biochemistry and Microbiology
>     Uppsala University, Sweden
>     marc.hoepner at imbim.uu.se <mailto:marc.hoepner at imbim.uu.se>
>
>
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>


-- 
-----------
Marc P. Hoeppner, PhD
Researcher
Department of Medical Biochemistry and Microbiology
Uppsala University, Sweden
marc.hoepner at imbim.uu.se

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