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Hi Marc,
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<div>The masked genome sequence is stored in the "theVoid" directory for each scaffold. There are files "query.fasta", "query.masked.fasta", and "query.masked.gff". The masked sequence is in the query.masked.fasta file and the genomic locations of the masked
regions are stored in the query.masked.gff. </div>
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<div>~Daniel</div>
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<div><span style="font-family: Tahoma; font-size: small; ">Daniel Ence</span></div>
<div><span style="font-family: Tahoma; font-size: small; ">Graduate Student</span></div>
<div><a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">Eccles Institute of Human Genetics</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">University of Utah</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">15 North 2030 East, Room 2100</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">Salt Lake City, UT 84112-5330</span></div>
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<div>On Jun 9, 2014, at 2:48 AM, Marc Höppner <<a href="mailto:marc.hoeppner@imbim.uu.se">marc.hoeppner@imbim.uu.se</a>></div>
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<blockquote type="cite">Hi,<br>
<br>
this may be an odd question, but I was wondering where, if at all, Maker reports the repeat-masked genome sequence? As far as I can tell the fasta sequences included in the gff annotation are unmasked (?) or at least not softmasked. I guess it wouldn’t be too
hard to take the repeat masker features and use them to soft mask the assembly, but still...<br>
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Regards,<br>
<br>
Marc<br>
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Marc P. Hoeppner, PhD<br>
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Department for Medical Biochemistry and Microbiology<br>
Uppsala University, Sweden<br>
<a href="mailto:marc.hoeppner@imbim.uu.se">marc.hoeppner@imbim.uu.se</a><br>
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