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  • gene_x
    Senior Member
    • May 2010
    • 108

    #1

    Why a sequence has 4 lines in fastq format

    As you know, the general format for fastq files have four lines:
    1st: @ with optional sequence identifier
    2nd: sequence
    3rd: + with optional sequence identifier
    4th: quality score for sequence in 2nd line

    The 3rd line doesn't really convey any useful information... do you know why is it included?
  • dkatzel
    Junior Member
    • Mar 2013
    • 5

    #2
    the format doesn't actually require 4 lines. Valid fastq files can be more than 4 lines with the sequence and quality values spread of several lines each. The quality header is used to tell you "there's no more sequence data left". Also since there are several quality encodings, it would be hard to tell where the quality starts otherwise if you didn't know the quality encoding.

    Comment

    • JohnN
      Member
      • Jan 2011
      • 31

      #3
      Originally posted by gene_x View Post
      As you know, the general format for fastq files have four lines:
      1st: @ with optional sequence identifier
      2nd: sequence
      3rd: + with optional sequence identifier
      4th: quality score for sequence in 2nd line

      The 3rd line doesn't really convey any useful information... do you know why is it included?
      To make it easy for lazy programmers like me to know when bases have stopped and quality scores have started? Especially when line feeds can't be trusted?

      Comment

      • maubp
        Peter (Biopython etc)
        • Jul 2009
        • 1544

        #4
        FASTQ was invented a long time ago, and was initially used with longer Sanger reads where line wrapping was a nice feature.

        See also http://dx.doi.org/10.1093/nar/gkp1137

        Comment

        • gene_x
          Senior Member
          • May 2010
          • 108

          #5
          Originally posted by maubp View Post
          FASTQ was invented a long time ago, and was initially used with longer Sanger reads where line wrapping was a nice feature.

          See also http://dx.doi.org/10.1093/nar/gkp1137
          What is this line wrap? Is it something like \n ?

          Comment

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