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Old 07-25-2012, 02:59 PM   #1
Arupsss
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Location: Trento, Italy

Join Date: May 2011
Posts: 44
Question BWA -N options

I am using BWA tool to find alignment of reads:

Now, I use the command:

./bwa aln -n 2 -k 41 DB.fa SRR493081_1.fastq > aln_sa.sai

However, there is another option in bwa i.e.

-N : Disable iterative search. All hits with no more than maxDiff
differences will be found. This mode is much slower than the default.

Should I use it means, is it will give more alignment without using it
(or more accuracy) ?

Thanks.
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