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  • #1

    SAM output from bowtie/crossbow

    I'm looking to get SAM output from bowtie, but taking advantage of the align.pl scripts developed for crossbow (I'm working in EC2).

    swapping the columns into what I think is standard bowtie and then running bowtie2sam from samtools is giving me numerous errors (the same method run on sam output direct from bowtie works).

    So is there an easy way to just get Sam from Align.pl?
    Tags: bowtie, crossbow, sam
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