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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Barry Moore [mailto:barry.utah@gmail.com] <br><b>Sent:</b> Monday, February 10, 2014 11:22 AM<br><b>To:</b> Aaron Liston<br><b>Cc:</b> maker-devel@yandell-lab.org<br><b>Subject:</b> Re: [maker-devel] Re-using repeat masking in SNAP training<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Arron,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Barry<o:p></o:p></p><div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>On Feb 8, 2014, at 7:08 PM, Aaron Liston wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><p class=MsoNormal>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<br><br><br>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>Barry Moore<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>Research Scientist<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>Dept. of Human Genetics<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>University of Utah<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>Salt Lake City, UT 84112<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>--------------------------------------------<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>(801) 585-3543<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p></div></div><div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>