[maker-devel] Maker: Re-annotation

[Carson Holt]

What does it do?

--Carson

From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Wednesday, 5 June, 2013 12:28 PM
To:  Carson Holt <carson.holt at oicr.on.ca>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>, Barry
Moore <barry.utah at gmail.com>
Subject:  Re: [maker-devel] Maker: Re-annotation

I upgraded to 2.28 and Maker is not running. Thanks!


On Wed, May 22, 2013 at 9:03 AM, Carson Holt <Carson.Holt at oicr.on.ca> wrote:
> 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>
> Date: Wednesday, 22 May, 2013 8:47 AM
> To: Barry Moore <barry.utah at gmail.com>
> Cc: <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> 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>
>>> _______________________________________________
>>> 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 <tel:%28801%29%20585-3543>
>> 
>> 
>> 
>> 
> 
> 
> 
> -- 
> 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 <tel:612-624-0532>



-- 
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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