Bowtie manual clearly says the default mode is to report one alignment per read, and it will be random choice when tied.
BWA doesn't seem to be quite clear at this point in its manual. Can anyone explain to me how BWA reports alignments if a read can be mapped to multiple locations? If I want it to report only one, which parameter should I use for that?
I'm particularly asking for BWA aln because I'm mapping 50bp SE reads. But it would be even better if you could also explain for BWA mem if it's different.
Thanks a lot!
BWA doesn't seem to be quite clear at this point in its manual. Can anyone explain to me how BWA reports alignments if a read can be mapped to multiple locations? If I want it to report only one, which parameter should I use for that?
I'm particularly asking for BWA aln because I'm mapping 50bp SE reads. But it would be even better if you could also explain for BWA mem if it's different.
Thanks a lot!
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