[maker-devel] Maker: Re-annotation

[Innocent Onsongo]

No. The MAKER produced GFF3 file does not contain any annotations. I even
tried setting the keep_preds parameter to 1 (keep_preds=1) to see if it
will pass annotations from the Augustus produced GFF file into the final
annotation but that didn't work. I have attached the maker_opts.ctl file I
used together with the first 100 lines of the GFF files it's using. I also
include the GFF file produced by MAKER (CGS01058First100.gff)




On Tue, May 21, 2013 at 10:43 PM, Barry Moore <barry.utah at gmail.com> wrote:

> Hi Getiria,
>
> Does the MAKER produced GFF3 file contain any annotations at all?  Can you
> send the first ~100 lines each of the MAKER produced GFF3 file and of the
> GFF3 files that you passed via maker_opts.ctl?
>
> B
>
> On May 21, 2013, at 9:58 AM, Innocent Onsongo wrote:
>
> Maker Development Team,
>
> I am trying to use Maker for re-annotation using  gene predictions from
> Augustus. We had previously used Augustus for gene prediction but now want
> to combine these annotations with some EST data. I updated
> fields maker_opts.ctl  as below
>
> genome=CGS01058.fasta #genome sequence file in fasta format
> est_gff=EST2Scaffold.gff3 # ESTs mapped to CGS01058.fasta using BLAT
> pred_gff=Augustus.gff3 #ab-initio predictions from
> other_gff=Promoters.gff3 #promoter annotations
> other_gff=CpG_Islands.gff3 # CpG island annotations
>
> Maker runs to completion and according to the log file annotation was
> successful. However, it also gives a "Segmentation fault (core dumped)"
> message. It does produce a GFF3 file but when I load the GFF3 file into IGV
> and look it does not contain any of the exon definitions in Augustus.gff3.
> Am I missing something?
>
> Regards,
> Getiria
>
> --
> Getiria Onsongo, Ph.D.
> Informatics Analyst, Research Informatics Support System
> Minnesota Supercomputing Institute for Advanced Computational Research
> University of Minnesota
> Minneapolis, MN 55455
> Phone: 612-624-0532
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
>


-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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