Hi,
I'm using BWA to map my short sequencing reads (Illumina MiSeq) on a reference sequence. Is this possible to set the minimum % of identity with BWA? For exemple, if I set 90%, then all reads under this threshold will be discarded. I know the parameter "-n" can do something like this but the manual is not really clear (for me). Is "-n" the minimal absolute mismatch in term of base pairs?
Thank you!
Antony
I'm using BWA to map my short sequencing reads (Illumina MiSeq) on a reference sequence. Is this possible to set the minimum % of identity with BWA? For exemple, if I set 90%, then all reads under this threshold will be discarded. I know the parameter "-n" can do something like this but the manual is not really clear (for me). Is "-n" the minimal absolute mismatch in term of base pairs?
Thank you!
Antony
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