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    Hi,

    I have a 3 columns file (conting name, lenght, number of reads).

    How can I select the only contigs that are at least 500nt in lenght and that have at least 1000 reads mapping?

    Is there a command to do that, even in different steps?

    Thanks

  • #2
    If your file is tab separated following will work. If you have some other field separator then change \t accordingly. Following assumes that you only have numbers in columns 2 and 3.

    Code:
    $ awk -F'\t' '{ if ($2 >= 500 && $3 >= 1000) print $0}' your_file
    If above does not work then post a small sample of your file.

    Comment


    • #3
      It works perfect!

      Comment

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