[maker-devel] Maker: Re-annotation

[Carson Holt]

Gotcha :-)

--Carson



From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Wednesday, 5 June, 2013 12:37 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Carson Holt <carson.holt at oicr.on.ca>, "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

Oops! I meant to type Maker is NOW running.


On Wed, Jun 5, 2013 at 9:30 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 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 <tel:612-624-0532>
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org



-- 
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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