Reporting policy of equally good alignments

2011-03-25
2013-06-05
  • Hello

    If a reference sequence contains both the sense and antisense sequence of a feature (e.g. a hairpin), does bowtie randomly select the alignment to report for a perfectly matching read, or does it have a preference for one strand or the other (e.g. sense over antisense)?

    Thanks,
    ken

     
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