Get all best hits- bowtie2
Hello, I'm trying to get all best-hits per read using bowtie2. It seems that the default will report the best one but will choose one in case of ties by default. I can try also set -k for limiting the number of hits or -a for all hits. Is there a way to get all best hits (one and all in case of ties), I did not found such option in the manual...
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