<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body><div><div style="font-family:Calibri,sans-serif;font-size:11pt">Dear Carson,<br><br>Yes that's what I did actually. But it seems that I only got much fewer gene models for est2genome and protein2genome in this way than I would expect. I have turned on EVM for my maker run. Could this explain the low numbers of est2genome and protein2genome models that I got? Thx!<br><br>Best,<br>Jia-Xing<br><br>Sent from my Nokia Lumia 920<br></div></div><div dir="ltr"><hr><span style="font-family:Calibri,sans-serif;font-size:11pt;font-weight:bold">From: </span><span style="font-family:Calibri,sans-serif;font-size:11pt"><a href="mailto:carsonhh@gmail.com">Carson Holt</a></span><br><span style="font-family:Calibri,sans-serif;font-size:11pt;font-weight:bold">Sent: </span><span style="font-family:Calibri,sans-serif;font-size:11pt">30/01/2018 18:06</span><br><span style="font-family:Calibri,sans-serif;font-size:11pt;font-weight:bold">To: </span><span style="font-family:Calibri,sans-serif;font-size:11pt"><a href="mailto:yuejiaxing@gmail.com">Jia-Xing Yue</a></span><br><span style="font-family:Calibri,sans-serif;font-size:11pt;font-weight:bold">Cc: </span><span style="font-family:Calibri,sans-serif;font-size:11pt"><a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org List</a></span><br><span style="font-family:Calibri,sans-serif;font-size:11pt;font-weight:bold">Subject: </span><span style="font-family:Calibri,sans-serif;font-size:11pt">Re: [maker-devel] Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?</span><br><br></div></body></html><html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap:break-word;line-break:after-white-space" class="">MAKER models will al have ‘maker’ in the source column. Everything else is a reference alignment (not a model). But you can grep on the gene name. If it is sourced from SNAP, it will have snap in the name, and the same is true for augustus, est2genome, protein2genome, etc.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 30, 2018, at 10:03 AM, Jia-Xing Yue <<a href="mailto:yuejiaxing@gmail.com" class="">yuejiaxing@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Dear Carson,<br class=""><br class=""></div>Thanks for the quick response! Could you elaborate a bit on on "grep on the name". Do you mean just grep all the lines in the gff_merge output with "est2genome" and "protein2genome" in column 3? In that case, what I got is the alignments rather than the gene model guessed by Maker based on the alignment, right? <br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thanks!<br class=""></div><div class=""><br class=""></div>Best,<br class=""></div>Jia-Xing<br class=""><br class=""><br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Jan 30, 2018 at 5:57 PM, 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">You can just grep on the name. Although est2genome and protein2genome should only be used for initial training, as they are almost always guaranteed to be partial and should be disabled once you have trained gene predictors that can build complete models.<br class="">
<br class="">
—Carson<br class="">
<div class=""><div class="h5"><br class="">
> On Jan 30, 2018, at 9:32 AM, Jia-Xing Yue <<a href="mailto:yuejiaxing@gmail.com" class="">yuejiaxing@gmail.com</a>> wrote:<br class="">
><br class="">
> Hello,<br class="">
><br class="">
> I enabled the est2genome and protein2genome option for Maker-3.00.0-beta in my particular case. I was wondering if it is possible to extract the gene models predicted by snap, augustus, est2genome, and protein2genome respectively.<br class="">
><br class="">
> By using the gff_merge command, I think I can extract some gene models for each cases but not all, especially for the est2genome and protein2genome set (e.g. those labeled with "maker-chr*-exonerate_<wbr class="">est2genome-gene" and "maker-chr*-exonerate_<wbr class="">protein2genome-gene").<br class="">
><br class="">
> Thanks in advance!<br class="">
><br class="">
> Best,<br class="">
> Jia-Xing<br class="">
><br class="">
><br class="">
><br class="">
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</blockquote></div><br class=""><br clear="all" class=""><br class="">-- <br 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 dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><span style="" class="">Jia-Xing Yue <br class=""><br class=""></span></div><div class=""><span style="" class="">Population Genomics and Complex Traits Group</span></div><div class=""><span style="" class=""><font size="2" face="arial, helvetica, sans-serif" class="">Tour Pasteur 8eme etage</font></span><span style="" class=""><div class=""><font size="2" face="arial, helvetica, sans-serif" class="">Faculté de Médecine<br class=""></font><span class=""><div class=""><font size="2" face="arial, helvetica, sans-serif" class="">Institute for Research on Cancer and Aging, Nice (IRCAN)</font></div><div class=""><font size="2" face="arial, helvetica, sans-serif" class="">CNRS UMR 7284 - INSERM U 1081 - </font>Université Côte d’Azur (UCA)</div></span><span class=""><span style="" class=""><font size="2" face="arial, helvetica, sans-serif" class=""><a href="https://maps.google.com/?q=28+Avenue+de+Valombrose&entry=gmail&source=g" target="_blank" class="">28 Avenue de Valombrose</a></font></span></span></div><div class=""><font size="2" face="arial, helvetica, sans-serif" class="">06107 NICE Cedex 2</font></div><div class=""><font size="2" face="arial, helvetica, sans-serif" class="">France</font></div></span></div><div class=""><br class=""></div><div class="">Twitter: <a href="https://twitter.com/iAmphioxus" target="_blank" class="">@iAmphioxus</a><br class=""></div><div class=""><div class="">Personal website: <a href="http://www.iamphioxus.org/" target="_blank" class="">http://www.iamphioxus.org/</a></div><div class="">Lab website: <a href="https://litilab.wordpress.com/" target="_blank" class="">https://litilab.wordpress.com/</a><br class=""></div><div class="">Yeast Population Reference Panel: <a href="https://yjx1217.github.io/Yeast_PacBio_2016/welcome/" target="_blank" class="">https://yjx1217.github.io/Yeast_PacBio_2016/welcome/</a></div><div class=""><br class=""></div><div class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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