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Old 08-01-2010, 12:36 AM   #1
genelab
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Default Mismatch setting in BWA

Helllo everyone,

I am still comfused how to set the maximum mismatch to 2 when I use "bwa aln", given 75bp reads.

bwa aln -n 2
or
bwa -l 75 -k 2

Any suggestions will be highly appreciated

Last edited by genelab; 08-03-2010 at 05:10 PM.
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Old 08-03-2010, 05:12 PM   #2
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could anybody help me to answer this question? thanks!
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Old 08-03-2010, 06:14 PM   #3
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Those are equivalent for 75 bp reads.
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Old 08-03-2010, 09:59 PM   #4
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Quote:
Originally Posted by adamdeluca View Post
Those are equivalent for 75 bp reads.
How about the read length not equal to 75, such as 50 or 100bp?

Thanks for your kindly reply
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Old 08-04-2010, 04:02 AM   #5
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-n 2 is equivalent to -l READ_LENGTH -k 2
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