[maker-devel] Maker: Re-annotation

[Innocent Onsongo]

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
>>> _______________________________________________
>>> 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
>>
>
>
>
> --
> 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
>



-- 
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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