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

[Barry Moore]

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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