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Old 01-15-2014, 08:46 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076
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First part could be explained by having adapter/primer dimers without any insert.

As for trimming give "trimmomatic" (http://www.usadellab.org/cms/?page=trimmomatic) or cutadapt (http://code.google.com/p/cutadapt/)/trimgalore (http://www.bioinformatics.babraham.a...s/trim_galore/) a try. Recent comparison of trimmers available http://www.plosone.org/article/info:...l.pone.0085024.
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