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  • JohnK
    Senior Member
    • Feb 2010
    • 106
    #1

    Optimal params for Bowtie

    Hi, I'm hoping this isn't a re-post (maybe I didn't search the right keywords), but I'm looking for optimal parameters for some Illumina paired-end data I'd like to map via Bowtie. Does anyone have any suggestions? Thank you for your help!

    J
    Tags: None
  • csoong
    Member
    • Jun 2009
    • 74
    #2
    unfortunately John, there is no optimal parameters it all depends on what you're looking for. it may sound crazy -- good luck!

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