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.
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.