<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="">Yes. It takes a the subset of RepBase. If runtime isn’t an issue and you really want to mask as much as possible, you can also set model_org=all. Most of whatever else is in RepBase probably won’t align anywhere, but it may give you marginally better sensitivity.<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 17, 2015, at 11:20 AM, 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 set<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="">model_org=picea</code>. I see that it created a new data base in the RepeatModeler folder<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="">Libraries/20140131/picea/specieslib</code>. What is the effect of 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;" class="">model_org</code><span class="Apple-converted-space"> </span>option? Does it extract sequences from RepBase that match the string<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="">picea</code>?</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></div><div class="bloop_original_html" 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);"><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class=""><br class=""></div><br class=""><div id="bloop_sign_1437153523647433984" 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><br class=""><p class="airmail_on" style="margin: 15px 0px;">On 2015-July-17 at 9:40:58 , Carson Holt (<a href="mailto:carsonhh@gmail.com" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;" class="">carsonhh@gmail.com</a>) wrote:</p><blockquote type="cite" class="clean_bq" style="margin: 15px 0px;"><span style="margin-top: 0px; margin-bottom: 0px;" class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class=""></div><div class="">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 class=""><blockquote type="cite" class="" style="margin: 15px 0px;"><div class="" style="margin-top: 0px;">On Jul 16, 2015, at 5:25 PM, Shaun Jackman <<a href="mailto:sjackman@gmail.com" class="" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;">sjackman@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class="" style="margin-bottom: 0px;"><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 class="" style="margin: 15px 0px; -webkit-margin-before: 0px;">Hi, Carson.</p><p class="" style="margin: 15px 0px;">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 class="" 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;">atp8</code><span class="Apple-converted-space"> </span>gene, but these genes were not in the contaminant contigs.</p><p class="" style="margin: 15px 0px;">I figured out that it’s because I’m running RepeatModeler to create the<span class="Apple-converted-space"> </span><code class="" 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;">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 class="" 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;">atp8</code><span class="Apple-converted-space"> </span>as being a LTR/Gypsy repeat.</p><p class="" style="margin: 15px 0px;">Any thoughts on why removing two contigs would cause RepeatModeler to identify new repeats?</p><p class="" style="margin: 15px 0px;">Cheers,<br class="" style="-webkit-margin-before: 0px;">Shaun</p><div class="" style="margin: 15px 0px;"><br class="webkit-block-placeholder" style="-webkit-margin-before: 0px;"></div></div><div class="bloop_original_html" style="font-family: Helvetica, Arial; 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