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Old 02-06-2014, 01:45 PM   #2
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Location: San Francisco, CA

Join Date: Feb 2011
Posts: 286

Does it actually warn you that those abundancies are something to worry about? The plot is just just show the relative frequency to the most abundant kmer, so if that most abundant kmer is very low, it shouldn’t be an issue.

Anyway, for chip-seq, I wouldn’t worry about this anyway, so long as your mappable fraction of the reads is within norms.
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