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  • Basic problem while using BWA

    I have other recent post asking for the convenience of using BWA-SW for some kind of database.

    While I am waiting for your great help, I tried to get into the algorithm. But I have not be able.

    I work with mac, and I was trying to work BWA in the terminal window.
    First, I unzipped the .tar file that I have downloaded from the BWA webpage and copy all its content to a folder.
    Then, I opened 'Terminal' and in the prompt I got into that folder. Once there, I wrote the following:

    bwa index -p unite -a bwtsw -c unite.fungal.fasta

    And after that a message appeared, saying:

    -bash: bwa: command not found


    What am I doing wrong??

    Thanks

  • #2
    If I am not mistaken (been a while since I installed BWA); you have to compile it first.

    Try typing make while being in the bwa directory.

    And if you are working on mac; you may wanna read this: http://seqanswers.com/forums/showthread.php?t=24133
    Last edited by TabeaK; 12-12-2012, 11:19 AM.

    Comment


    • #3
      Thanks a lot.

      I'll try what you say and read that page inmediatly and I'll write back then.

      Comment

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