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

[Carson Holt]

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>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
>
>
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