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  • fastq to fasta conversion

    How can I convert my fastq files to two fasta files with one containing the reads and another containing the quality scores?

    Thanks

  • #2
    You could use awk to create a simple fasta file from your fastq, e.g.

    awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' my.fastq > my.fasta

    However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.

    Comment


    • #3
      Originally posted by Bio.X2Y View Post
      However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.
      ... and their corresponding qualities ..

      mySeq.fasta :
      >mySeq
      ACGTACGT

      mySeq.fasta.qual:
      >mySeq
      22 22 33 33 22 22 33 44

      There are still some programs which need to be fed with fasta/qual :-)

      Anyway, qualities need to be converted to phred-stye ..

      Comment


      • #4
        Thanks sklages! I wasn't aware of qual files.

        kwtennis311, there seem to be some existing posts on this, you might find answers in this, e.g. http://seqanswers.com/forums/showthread.php?t=3730.

        Comment


        • #5
          thanks

          thanks guys, Biopython did the trick

          Comment

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