[maker-devel] split genes

[Carson Holt]

MAKER will not try and predict a gene across contigs because it it too difficult to determine contig order. If you are able to determine order, then it is best to merge the contigs into a single scaffold before annotating rather than try and produce split models in GFF3.

—Carson

> On Mar 16, 2017, at 9:48 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello:
> 
> If one gene was covered by two contigs, sometimes we may predicted two genes. I wonder how Maker deal with such conditions?
> Even Maker tried to reduce such cases, they can not be completely avoid. So I wonder whether there is any way or any tool to find such split genes (one gene split into two contigs and predicted as two genes)?
> 
> As we know, we can also provide protein sequences and transcript assembly as evidences. Can a protein sequence or transcript assembly rescue the split genes in Maker pipe line? For example, if one transcript cover 40% of predicted genes predicted in two contigs, then merge the predicted genes into one?
> 
> Thanks
> 
> Best
> Quanwei
> 
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