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Bowtie2 Bug: error reporting multiple alignments

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  • Bowtie2 Bug: error reporting multiple alignments

    Hi,

    I think I've found a problem with reporting multiple alignments in Bowtie2, and was wondering if anyone else can confirm.


    I often specify a -k value to report multiple alignments in my .SAM file. However, I have found that by default the SEQ and QUAL string are asterisks, even without calling the following parameter:

    "--omit-sec-seq

    When printing secondary alignments, Bowtie 2 by default will write out the SEQ and QUAL strings. Specifying this option causes Bowtie 2 to print an asterix in those fields instead."


    I would very much like for Bowtie2 to report the SEQ and QUAL strings, and was wondering if anyone knows how to solve this, or has at least encountered this problem before.

    Thanks!
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