Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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?

  • #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


    • #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


      • #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


        • #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

          Latest Articles

          Collapse

          • seqadmin
            Recent Advances in Sequencing Analysis Tools
            by seqadmin


            The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
            05-06-2024, 07:48 AM
          • seqadmin
            Essential Discoveries and Tools in Epitranscriptomics
            by seqadmin




            The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
            04-22-2024, 07:01 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 07:03 AM
          0 responses
          14 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-10-2024, 06:35 AM
          0 responses
          36 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-09-2024, 02:46 PM
          0 responses
          43 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-07-2024, 06:57 AM
          0 responses
          38 views
          0 likes
          Last Post seqadmin  
          Working...
          X