[maker-devel] Re-using repeat masking in SNAP training

[Barry Moore]

Yep.  If you want to keep the results from each step just copy the GFF3 file from your first run to a new name and then redo your run.

B

On Feb 10, 2014, at 12:46 PM, Aaron Liston wrote:

> Hi Barry:   I changed the name of the genome file, so that I could see the results at each step. However, it sounds like if I had kept the same name, MAKER would use the info from the previous run.  Is that correct?  Aaron
>  
> From: Barry Moore [mailto:barry.utah at gmail.com] 
> Sent: Monday, February 10, 2014 11:22 AM
> To: Aaron Liston
> Cc: maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] Re-using repeat masking in SNAP training
>  
> Hi Arron,
>  
> If you re-run maker and don't change the details about the repeat library (i.e. you only update the SNAP HMM file) then MAKER shouldn't redo any work with repeat masking it should reuse the work it has already done.  Is this not what you are seeing?
>  
> Barry
>  
>  
> On Feb 8, 2014, at 7:08 PM, Aaron Liston wrote:
> 
> 
> I am following the tutorial for training SNAP, and it works fine. However, the tutorial instructions have MAKER repeat the repeat masking. To avoid this, I concatenated my gff files from the first round of annotation and used maker_gff=round1.gff and rm_pass=1  but at the end of the process, the repeat annotations were not there. Any suggestions?  Thanks, Aaron
> 
> 
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>  
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>  
>  
>  
>  

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543



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