Hi,
I've used bwa for 35bp solexa read with following option
"-n 20 -l 15 -k 0 -t 12"
to get reads having perfect match at the first 15bp. And then
I generated .sam file by using "bwa samse" but there are
some reads I did not expected as follwoing.
MD:Z:14A10A0T1A1C0A0G0A0T0
MD:Z:12^G7^AAC0C4G1T1
I would like to know if there is minimum value for "-l" option. Or
this is an alignment problem after mapping.
BWA version is 0.5.7
Thanks,
corthay
I've used bwa for 35bp solexa read with following option
"-n 20 -l 15 -k 0 -t 12"
to get reads having perfect match at the first 15bp. And then
I generated .sam file by using "bwa samse" but there are
some reads I did not expected as follwoing.
MD:Z:14A10A0T1A1C0A0G0A0T0
MD:Z:12^G7^AAC0C4G1T1
I would like to know if there is minimum value for "-l" option. Or
this is an alignment problem after mapping.
BWA version is 0.5.7
Thanks,
corthay
