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Old 08-07-2011, 12:37 PM   #1
Location: Seattle

Join Date: Jul 2011
Posts: 98
Default multiple alignments with BWA

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?


efoss is offline   Reply With Quote

bwa, multiple alignments, multiple hits

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