[maker-devel] Maker: Re-annotation

[Carson Holt]

Are you using MAKER version 2.10? I ask because there is in issue with other_gff in that version that has since been fixed.  So if you don't get other_gff to pass-through, you will need to upgrade to 2.28 (release date is later today coincidentally).

For the Augustus GFF3 file, the format is a little weird which is causing the problem.  They are mRNA features not attached to genes.  Rather than build the expected 3 level gene/mRNA/exon structure for these, it is simpler just to convert it to the 2 level match/match_part structure.  Just convert the 'mRNA' tag to 'match' and all 'exon' tags to 'match_part'.  Rename the GFF3 when your done so that it will force rebuild of the GFF3 database when you run again.

Thanks,
Carson



From: Innocent Onsongo <onson001 at umn.edu<mailto:onson001 at umn.edu>>
Date: Wednesday, 22 May, 2013 8:47 AM
To: Barry Moore <barry.utah at gmail.com<mailto:barry.utah at gmail.com>>
Cc: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Maker: Re-annotation

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<mailto: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<tel:612-624-0532>
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
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--
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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