<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">The names of scripts used are listed in the maker_exe.ctl file. It depends on if formatting or any flags have changed between versions.<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 20, 2017, at 1:59 AM, Ray Cui <<a href="mailto:rcui@age.mpg.de" class="">rcui@age.mpg.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear Carson,<div class=""><br class=""></div><div class=""> I have now run GeneMark-ET, and it produces a trained .mod file. I think it can be then passed to Maker. Do you know what is the final constructed command line in Maker that calls genemark? Genemark-et and es use the same perl script so one probably only needs to use the --prediction and --predict_with xxx.mod options to predict genes using the species specific parameters (bypassing regular training and prediction steps)</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Best Regards,</div><div class="">Ray</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Dr. Rongfeng (Ray) Cui</div><div class="">Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing</div><div class=""><span style="text-align:justify" class="">Wissenschaftlicher MA</span> / Postdoctoral researcher</div><div class="">Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne</div><div class="">Postal address: Postfach 41 06 23, D-50866 Köln / Cologne</div><div class="">Tel.:+49 (0)221 496 </div><div class="">Mobile: +49 <a value="+4922137970496" style="color:rgb(17,85,204)" class="">0221 37970 496</a></div><div class=""><a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a></div><div class=""><a href="http://www.age.mpg.de/" target="_blank" class="">www.age.mpg.de</a> </div><div class=""><br class=""></div></div><div class=""><br class=""></div></div><div class=""></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Mon, Feb 20, 2017 at 6:39 AM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">MAKER was support was designed with GeneMark-ES. It may or may not work with GeneMark-ET. So any MAKER related archive posts etc. will be related to the latter.<div class=""><br class=""></div><div class="">With GeneMark-ES, you simply provided a genome assembly and let it run. It would then produce several files and output directories. The es.mod file was the one you provided to MAKER. I don’t know how this compares to GeneMark-ET.<span class="HOEnZb"><font color="#888888" class=""><br class=""><div class=""><br class=""></div></font></span><div class=""><span class="HOEnZb"><font color="#888888" class="">—Carson</font></span><div class=""><div class="h5"><br class=""><div class=""><br class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Feb 14, 2017, at 8:44 AM, Ray Cui <<a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a>> wrote:</div><br class="m_-228215818425102403Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Daniel,<div class=""><br class=""></div><div class=""> thanks! It seems that Genemark-ET has a "--training" flag, is that the flag I should use when training or should I just let Genemark also perform the prediction? </div><div class=""><br class=""></div><div class="">Ray</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-228215818425102403gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Dr. Rongfeng (Ray) Cui</div><div class="">Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing</div><div class=""><span style="text-align:justify" class="">Wissenschaftlicher MA</span> / Postdoctoral researcher</div><div class="">Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne</div><div class="">Postal address: Postfach 41 06 23, D-50866 Köln / Cologne</div><div class="">Tel.:<a href="tel:+49%20221%20496" value="+49221496" target="_blank" class="">+49 (0)221 496</a> </div><div class="">Mobile: +49 <a value="+4922137970496" style="color:rgb(17,85,204)" class="">0221 37970 496</a></div><div class=""><a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a></div><div class=""><a href="http://www.age.mpg.de/" target="_blank" class="">www.age.mpg.de</a> </div><div class=""><br class=""></div></div><div class=""><br class=""></div></div><div class=""></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Tue, Feb 14, 2017 at 3:43 PM, Ence,daniel <span dir="ltr" class=""><<a href="mailto:d.ence@ufl.edu" target="_blank" class="">d.ence@ufl.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">
Hi Ray,
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<div class="">I think you’re on the right track with training Genemark with RNAseq data. It should only change the training steps, which are external to MAKER, but not how MAKER runs Genemark. You’ll still give MAKER the path to the “es.mod" file made by Genemark. </div>
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<div class="">For the 2nd question, in the MAKER beta 3, MAKER creates a control file for EVM, in which you set your weights for the various inputs, and then MAKER runs EVM alongside all the other gene predictors and chooses the model that is best supported
by the evidence. </div>
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<div class="">~Daniel</div>
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<blockquote type="cite" class=""><div class=""><div class="m_-228215818425102403h5">
<div class="">On Feb 14, 2017, at 7:38 AM, Ray Cui <<a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a>> wrote:</div>
<br class="m_-228215818425102403m_2622219514221564884Apple-interchange-newline">
</div></div><div class=""><div class=""><div class="m_-228215818425102403h5">
<div dir="ltr" class="">Hello,
<div class=""><br class="">
</div>
<div class=""> I have sucessfully installed Maker beta 3, working with both Augustus and SNAP. I also want to try adding GeneMark-ES to the ab initio predictor.</div>
<div class=""> When I read the GeneMark-ES manual, it says that one can use RNAseq data to aid training. I'm wondering what would be the best way to integrate Genemark-ET predictions into Maker. Should I run Genemark-ET independent of Maker, then integrate
the GFF at some point during the maker process? If so, how should I edit the configuration file? Currently maker has an option called "gmhmm". Should I then train GeneMark by myself with RNAseq data, then feed the hmm to maker?</div>
<div class=""> </div>
<div class=""> And perhaps an unrelated question is that now Maker beta 3 supports EVM. I'm wondering how EVM is used by Maker (at which step, what does it do), and how does it differ from what Maker is designed for (both reconciles different gene
models). </div>
<div class=""><br class="">
</div>
<div class="">Best Regards,</div>
<div class="">Ray</div>
<div class=""><br class="">
</div>
<div class="">Dr. Rongfeng (Ray) Cui
<div class="">
<div class="m_-228215818425102403m_2622219514221564884gmail_signature">
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<div class="">Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing</div>
<div class=""><span style="text-align:justify" class="">Wissenschaftlicher MA</span> / Postdoctoral researcher</div>
<div class="">Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne</div>
<div class="">Postal address: Postfach 41 06 23, D-50866 Köln / Cologne</div>
<div class="">Tel.:<a href="tel:+49%20221%20496" value="+49221496" target="_blank" class="">+49 (0)221 496</a> </div>
<div class="">Mobile: +49 <a value="+4922137970496" style="color:rgb(17,85,204)" class="">0221 37970 496</a></div>
<div class=""><a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a></div>
<div class=""><a href="http://www.age.mpg.de/" target="_blank" class="">www.age.mpg.de</a> </div>
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