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Old 08-22-2011, 10:10 PM   #1
jay2008
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Default bowtie index file

in bowtie index file, each nt (A,C,T,G) is kept by 2 bits. but how to do with the fifth nt '$'?
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Old 09-15-2011, 01:42 AM   #2
[mic]
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As i know bowtie stores the $ as an A which must be intent at LF-mapping.

Anyone correct me if I'm wrong.
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