HI,
I am curious as what this exactly means:
bwa aln -n 1 -N ...
-n NUM Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]
-N Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.
I read the documentation of bwa but I couldn't figure out what the option -n 1 -N would mean.
Help would be appreciated.
thanks!
We had a very similar question before: A: What does BWA's '-n' parameter mean?
@Michael, thanks!