I am doing experiments with BWA and BowTie. Now, I am finding alignments using command:
./bwa aln -n 0 -k 41 database.fa SRR4493095_1.fastq > aln_sa.sai
and
./bwa samse database .fa aln_sa.sai SRR4493095_1.fastq > out_sa.sam
However, while BowTie gives 123 number of matches for 100 reads, BWA gives just 100 number of matches (one for each, does not reporting if match in another position found). Can anybody help me why is this happening and how to solve this ? I give -n 0 option because, I want to find matching allowing no mismatch.
Thanks in advance.
./bwa aln -n 0 -k 41 database.fa SRR4493095_1.fastq > aln_sa.sai
and
./bwa samse database .fa aln_sa.sai SRR4493095_1.fastq > out_sa.sam
However, while BowTie gives 123 number of matches for 100 reads, BWA gives just 100 number of matches (one for each, does not reporting if match in another position found). Can anybody help me why is this happening and how to solve this ? I give -n 0 option because, I want to find matching allowing no mismatch.
Thanks in advance.
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