<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="">I don’t know of any tool to analyze the repeat info. MAKER really only focuses on getting the masking done for the gene prediction, and while it does keep the repeats as features in the GFF3, it does not do any kind of analysis. You would have to do that outside of MAKER.<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 Sep 13, 2017, at 8:51 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Dear Carson:<br class=""><br class=""></div>We have generated species specific repeat library following your pipeline (<a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction--Basic" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction--Basic</a>). And did genome annotation by maker2 by using both species specific repeat library and mammalian repeat library. <br class=""><br class=""></div>Now, we want to do some comparison about the repeat contexts among different species. So I want to generate species specific for other species and also use both their species specific repeat library and mammalian repeat library. But I found, I can only provide either the species specific repeat library or mammalian repeat library to RepeatMasker (not for both). I wonder whether I can run maker2 on those genome but only for repeat masking. <br class=""><br class=""></div>BTW, by running RepeatMasker we can get a summary report (as below), I wonder whether there is any script from maker2 to analyze repeats element (or other tools to process the output of maker2). <br class=""><br class=""></div>Many thanks<br class=""><span style="color:rgb(0,0,255)" class=""><br class=""><br class="">file name: test_scaffold31.fasta <br class="">sequences: 1<br class="">total length: 863590 bp (858757 bp excl N/X-runs)<br class="">GC level: 37.02 %<br class="">bases masked: 301634 bp ( 34.93 %)<br class="">==================================================<br class=""> number of length percentage<br class=""> elements* occupied of sequence<br class="">--------------------------------------------------<br class="">SINEs: 134 14362 bp 1.66 %<br class=""> Alu/B1 28 2183 bp 0.25 %<br class=""> MIRs 21 2860 bp 0.33 %<br class=""><br class="">LINEs: 188 129104 bp 14.95 %<br class=""> LINE1 168 124633 bp 14.43 %<br class=""> LINE2 16 4266 bp 0.49 %<br class=""> L3/CR1 4 205 bp 0.02 %<br class=""> RTE 0 0 bp 0.00 %<br class=""><br class="">LTR elements: 127 101129 bp 11.71 %<br class=""> ERVL 10 3057 bp 0.35 %<br class=""> ERVL-MaLRs 22 6902 bp 0.80 %<br class=""> ERV_classI 66 80258 bp 9.29 %<br class=""> ERV_classII 29 10912 bp 1.26 %<br class=""><br class="">DNA elements: 27 4402 bp 0.51 %<br class=""> hAT-Charlie 13 1836 bp 0.21 %<br class=""> TcMar-Tigger 8 1651 bp 0.19 %<br class=""><br class="">Unclassified: 4 1590 bp 0.18 %<br class=""><br class="">Total interspersed repeats: 250587 bp 29.02 %<br class=""><br class=""><br class="">Small RNA: 9 616 bp 0.07 %<br class=""><br class="">Satellites: 66 40820 bp 4.73 %<br class="">Simple repeats: 159 7235 bp 0.84 %<br class="">Low complexity: 50 2766 bp 0.32 %<br class="">==================================================<br class=""><br class="">* most repeats fragmented by insertions or deletions<br class=""> have been counted as one element<br class=""> <br class=""><br class="">The query species was assumed to be mammalia <br class="">RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127<br class=""> <br class="">run with rmblastn version 2.2.27+</span> <br class=""></div>
</div></blockquote></div><br class=""></div></div></body></html>