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.error { color:#AA0000; }</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="bloop_markdown"><p>Hi, Carson.</p>
<p>I set <code>model_org=picea</code>. I see that it created a new data base in the RepeatModeler folder <code>Libraries/20140131/picea/specieslib</code>. What is the effect of the <code>model_org</code> option? Does it extract sequences from RepBase that match the string <code>picea</code>?</p>
<p>Cheers,<br>
Shaun</p>
<p></p></div><div class="bloop_original_html"><style>body{font-family:Helvetica,Arial;font-size:13px}</style><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div> <br> <div id="bloop_sign_1437153523647433984" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px">-- <br><a href="http://sjackman.ca/">http://sjackman.ca/</a></div></div> <br><p class="airmail_on" style="color:#000;">On 2015-July-17 at 9:40:58 , Carson Holt (<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div></div><div>
<title></title>
That is weird.
<div class=""><br class=""></div>
<div class="">One thought though. When you run MAKER do you
supply both rmlib and model_org or just rmlib? If you are only
supplying rmlib, you could try supplying both together
(RepeatMasker will then run twice). That way some of the edge
cases might better be identified.</div>
<div class=""><br class=""></div>
<div class="">—Carson</div>
<div class=""><br class="">
<div class=""><br class=""></div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Jul 16, 2015, at 5:25 PM, Shaun Jackman
<<a href="mailto:sjackman@gmail.com" class="">sjackman@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="bloop_markdown" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<p style="margin: 15px 0px; -webkit-margin-before: 0px;" class="">
Hi, Carson.</p>
<p style="margin: 15px 0px;" class="">I removed two small
contaminant contigs (~7 kbp) from the assembly (~6 Mbp), and MAKER
found four fewer genes, four copies of the same<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class="">atp8</code><span class="Apple-converted-space"> </span>gene, but these genes were not
in the contaminant contigs.</p>
<p style="margin: 15px 0px;" class="">I figured out that it’s
because I’m running RepeatModeler to create the<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class="">rmlib</code><span class="Apple-converted-space"> </span>for MAKER. When I remove the
contaminant contigs, RepeatModeler now identifies this
gene<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;" class="">atp8</code><span class="Apple-converted-space"> </span>as being a LTR/Gypsy
repeat.</p>
<p style="margin: 15px 0px;" class="">Any thoughts on why removing
two contigs would cause RepeatModeler to identify new repeats?</p>
<p style="margin: 15px 0px;" class="">Cheers,<br style="-webkit-margin-before: 0px;" class="">
Shaun</p>
<div style="margin: 15px 0px;" class=""><br class="webkit-block-placeholder"></div>
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<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class=""><br class=""></div>
<br class="">
<div id="bloop_sign_1437087480103544832" class="bloop_sign">
<div style="font-family: helvetica, arial; font-size: 13px;" class="">-- <br class="">
<a href="http://sjackman.ca/" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;" class="">http://sjackman.ca/</a></div>
</div>
</div>
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