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

[Aaron Liston]

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

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(801) 585-3543

 

 

 

 

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