[maker-devel] Single exon in GFF file.

[Carson Holt]

Single_exon=0 does not mean not to call single exon genes. It means not to use single exon ESTs as evidence support (as issues related to single exon ESTs are well known, so it is best to exclude them). You will still get single exon genes from the predictors and single exon protein alignments from your protein evidence. Every genome is expected to contain a number of single exon genes (the most conserved genes across species in fact tend to be single exon - there is evolutionary selection that favors single exon structure in essential genes).

What you will want to do is look at your contigs in a browser. Depending on the structure of the genes you see and the genes around them, you may conclude that you have insufficient repeat masking (results in repeats being called as genes). Or you may realize that the contigs in question are prokaryotic (i.e. assembly contamination), which must be resolved upstream of MAKER. Or they are real genes. Remember every genome is expected contain single exon genes.

—Carson



> On May 24, 2016, at 10:58 AM, Won C Yim <wyim at unr.edu> wrote:
> 
> Dear MAKER team,
> 
> We have been using MAKER to generate our plant genome annotations.
> 
> Even though I set the “single_exon=0”, there are a lot of single exon gene based on Eval 2.2.8.
> 
> Is there any way to discard single exon genes?
> 
> Regards,
> 
> Won
> 
> -- 
> Yim, Won Cheol
> MS330/Department of Biochemistry & Molecular Biology
> 1664 N. Virginia Street
> University of Nevada, Reno
> 
> email: wyim at unr.edu <mailto:wyim at unr.edu>
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