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Hi Xabier, MAKER offer several options for repeat-masking. There’s a file of repetitive element proteins that is run with repeat runner, and there you can run RepeatMasker with a custom library and/or one of the default RepeatMasker libraries.
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<div class="">The results from these programs are in the gff3 files that maker generates. Depending on the library that you give RepeatMasker, the repeats might be classified as to transposable element family and simple vs. complex repeats. These are probably
a good place to start, but you’ll have to extract that data from the gff3 file and compile it. </div>
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<div class="">Let us know whether that helps. </div>
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<div class="">Thanks,</div>
<div class="">Daniel</div>
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<div class="">On Mar 21, 2015, at 9:27 PM, Xabier Vázquez Campos <<a href="mailto:xvazquezc@gmail.com" class="">xvazquezc@gmail.com</a>> wrote:</div>
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<div class="">Hi all,<br class="">
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I was wondering how can I get data about the repeat content of the genome from maker if possible, as well as each type of repeats: RE, transposons, simple repeats, low complexity repeats<br class="">
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Thank you in advance,<br class="">
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Xabier<br clear="all" class="">
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-- <br class="">
<div class="gmail_signature">Xabier Vázquez Campos<br class="">
<i class="">PhD Candidate</i><br class="">
Water Research Centre<br class="">
School of Civil and Environmental Engineering<br class="">
The University of New South Wales<br class="">
Sydney NSW 2052 AUSTRALIA<br class="">
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