[maker-devel] split genes

[Fields, Christopher J]

Just curious but have you tried scaffolding your assembly using your RNA-Seq de novo assembly data?  We’ve seen some improvement with BUSCO calls and annotation after doing this using L_RNA_Scaffolder (though you do need to be a bit careful and try reducing your trx assembly down to a somewhat non-redundant set).

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Carson Holt <carsonhh at gmail.com>
Date: Tuesday, March 21, 2017 at 12:00 PM
To: Quanwei Zhang <qwzhang0601 at gmail.com>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] split genes

I have no suggestions, but maybe someone else on the list may have some.

—Carson


On Mar 17, 2017, at 11:49 AM, Quanwei Zhang <qwzhang0601 at gmail.com<mailto:qwzhang0601 at gmail.com>> wrote:

Thank you for your explanation. But do you have any suggestions on such issues? Is there any tools to detect such split genes or any other tool can even further improve the gene models obtained by Maker? Thanks.
Best
Quanwei

2017-03-17 11:21 GMT-04:00 Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>:
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<mailto: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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