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  • Shishir
    Member
    • Nov 2012
    • 22

    How to parse FASTQ file?

    I am new in NGS. I need to format some fastq files. For example I want to replace characters /1 and /2 with -1 and - 2 in the files having data like @HWUSI-EAS1671_0001:5:1:1022:10290/1.
    I tried to do it in perl with pattern matching but the files are too big to parse. Could anyone please give me suggestion on share any code?
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Have you considered using "awk"?

    Comment

    • Shishir
      Member
      • Nov 2012
      • 22

      #3
      Thanks!
      I searched for "awk" and realize "sed" can do it easily

      Comment

      • kopi-o
        Senior Member
        • Feb 2008
        • 319

        #4
        The files are surely not too big to parse with perl (for your purposes) if you do it right - you only need to have four lines at a time (or maybe just one) in memory. Also it might be a good opportunity to learn some BioPerl :-)

        Comment

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