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Old 10-01-2012, 10:59 AM   #1
ameyer
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Location: Toronto, ON

Join Date: Jan 2011
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Default Ambiguous bases vs mismatches in Tophat

Does Tophat treat ambiguous bases (N) in the reference as mismatches? In the Tophat manual -N/--read-mismatches is defaulted to 2 but there doesn't seem to be a parameter to set the number of allowable ambiguous matches in a read.
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ambiguous bases, rna-seq, tophat 2.0.3

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