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  • elisadouzi
    Member
    • Mar 2011
    • 20

    #1

    Using bam file as the input for velvet

    Has anyone tried to using bam file as the input for velvet? Can it automatically recognize the paired end information? I tried a little bit, seems velvet use it as single end reads.


    Thanks!
  • swbarnes2
    Senior Member
    • May 2008
    • 910

    #2
    Sure, it works fine. However, it will only recognize paired ends if the bam is sorted by read name, and not coordinate.

    Picard can do this if your .bam is already sorted.

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