<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 agree. Also a 100bp insert of N’s will essentially be ignored by aligners and predictors. They’ll jump across it as if it was just an intron, resulting in false merges and bad predictions.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 3, 2017, at 9:48 AM, Ence,daniel <<a href="mailto:d.ence@ufl.edu" class="">d.ence@ufl.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Hi Chao, I don’t think merging the contigs is a good idea. Unless you actually know the distances (in basepairs) between the contigs, this could lead to many spurious alignments. I think you should leave them separate in your fasta file for both repeatmodeler,
ab-initio training and running maker. If you’re worried about short contigs in your assembly, you can exclude shorter contigs with the min_contig option in the maker_opts control file.
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<div class="">~Daniel<br class="">
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<div class="">On Feb 28, 2017, at 2:43 AM, <a href="mailto:dcg@cau.edu.cn" class="">
dcg@cau.edu.cn</a> wrote:</div>
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<span class=""></span>Dear sir:</div>
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After assemblying, I got many contigs and their order in each chromosome.</div>
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What I have done is merging these contigs into each chromosomes followed by the order, with 100 Ns inserted betwwen each contigs. So that I got chr1 chr2......Then I ran the repeatmodeler, predictor to annotate it.</div>
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Could my way reach a high-quality result? Should I use all the contigs to mask repeats and practice predictor?</div>
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Is there any better way to do genome-wide annotation?</div>
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I'm looking forward to your reply!</div>
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Best wishes!</div>
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Chao Chao</div>
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<div style="margin: 10px; font-family: verdana; font-size: 10pt;" class="">2017.02.28</div>
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