[maker-devel] Merging 2 annotations

[Carson Holt]

This might be a round about way to get them to have the names unaltered.
Give the pred_gff ones to est_gff.  Still give the model_gff ones to
model_gff. Set est2genome=1 and single_exon=1.  Then add this line to the
control file est_forward=1.  This is normally used to move transcripts
forward onto new assemblies with names being drawn from the alignment, but
by telling MAKER that these are ESTs instead of predictions and setting the
appropriate values, it will think it's moving transcripts forward, and the
final result may be what you want.

--Carson

From:  Anthony Bretaudeau <anthony.bretaudeau at rennes.inra.fr>
Date:  Thursday, June 12, 2014 at 10:17 AM
To:  Daniel Ence <dence at genetics.utah.edu>
Cc:  Carson Holt <carsonhh at gmail.com>, "<maker-devel at yandell-lab.org>"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Merging 2 annotations

    
 Yes, I think that's why the ids get changed.
 But I don't know which predictions I want to keep as I'm using maker to
only keep the ones that are not equivalent to the models that are in the
model_gff.
 
 Anthony
 
 
On 12/06/2014 17:50, Daniel Ence wrote:
 
 
>   Hi Anthony, So I think that the gene ID gets changed in the process of
> promoting things from pred_gff to gene models. If you know which predictions
> you want to keep, then you can select those out and pass them to model_gff.
> 
>  
>  
> ~Daniel
>  
> 
>  
>  
> 
>  
>  
> Daniel Ence
>  
> Graduate Student
>  
> dence at genetics.utah.edu
>  Eccles Institute of Human Genetics
>  University of Utah
>  15 North 2030 East, Room 2100
>  Salt Lake City, UT 84112-5330
>  
>  
>  
>  
> On Jun 12, 2014, at 7:00 AM, Anthony Bretaudeau
> <anthony.bretaudeau at rennes.inra.fr>
>  
>  wrote:
>  
>  
>> A little question which is related: I set the map_forward option to 1, but it
>> seems to work only for the model_gff gff. Is there a way to make it keep the
>> original IDs also for the pred_gff file?
>>  
>  
>  
>  
>  
 
 


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