The manuscript "Fast and accurate short read alignment with Burrows–Wheeler transform" says this:
"It [BWA] performs gapped alignment for single- end reads, supports paired-end mapping, generates mapping quality and gives multiple hits if required."
I would like to use identify all reasonable alignments for my reads, since if I see a read aligning to many places in the genome, I know to be skeptical of that alignment. However, I don't see this option in BWA. Can anyone help me out here?
Thanks.
Eric
"It [BWA] performs gapped alignment for single- end reads, supports paired-end mapping, generates mapping quality and gives multiple hits if required."
I would like to use identify all reasonable alignments for my reads, since if I see a read aligning to many places in the genome, I know to be skeptical of that alignment. However, I don't see this option in BWA. Can anyone help me out here?
Thanks.
Eric