[maker-devel] Maker: Re-annotation

[Innocent Onsongo]

One other thing, I ran MAKER with the RM_off flag (maker -f -RM_off -q) the
input sequences had already been masked.



On Wed, May 22, 2013 at 7:47 AM, Innocent Onsongo <onson001 at umn.edu> wrote:

> 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
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