[maker-devel] Maker: Re-annotation

[Barry Moore]

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
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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