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  • viv
    Junior Member
    • Aug 2014
    • 3

    #1

    Problem with Building Index with Bowtie

    I am new to the field, so I have downloaded chromFA.tar.gz from UCSC and unzipped it. Now I want to combine the files and I have tried both following commands:
    cat *.fa > hg19.fa
    sudo cat *.fa > hg19.fa

    And I am getting the same error:
    -bash hg19.fa: Permission denied

    So what should I do now?
    Thanks in advance for your help.
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478

    #2
    Do you have write permissions in that directory? Presumably not. Do you have sudo privileges?

    Comment

    • ulduz
      Junior Member
      • Oct 2012
      • 3

      #3
      I should have. Because this is from our common cluster between several labs. I am not the only one who is performing mapping.

      Comment

      • dpryan
        Devon Ryan
        • Jul 2011
        • 3478

        #4
        A quick "ls -la" would confirm the source of the problem. BTW, you can also just ask your local IT people, since this ends up having nothing to do with bioinformatics.

        Comment

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