split genes

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

split genes

Quanwei Zhang
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


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: split genes

Carson Holt-2
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 <[hidden email]> 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
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: split genes

Quanwei Zhang
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 <[hidden email]>:
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 <[hidden email]> 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
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: split genes

Carson Holt-2
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 <[hidden email]> 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 <[hidden email]>:
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 <[hidden email]> 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
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: 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 <[hidden email]> on behalf of Carson Holt <[hidden email]>
Date: Tuesday, March 21, 2017 at 12:00 PM
To: Quanwei Zhang <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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 <[hidden email]>:

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 <[hidden email]> 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
>

> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

 

 


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Loading...