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  • Missing header Fastq file

    Hello,

    I have a fastq file that is missing the header information for 70% of the reads. It is usually the information that starts with an @ and gives the sequencer id plus genomic coordinates. Anyone else have an issue like this and is this fixable. The sample is very old.

    Thanks,
    Nino

  • #2
    That sounds more like a SAM file than a FASTQ file.

    Comment


    • #3
      No it is not a Sam file. A fastq file consists of a header from the machine it was sequence include genomic coordinates plus other information, second line consists of the read itself, third line which strand position, and lastly fourth line the base quality score. Have you ever looked into a fastq file before? Sam files hold much much more detailed information.

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      • #4
        I am not sure if that would be fixable unless you had the images/intensities from original run and could do the basecalling again to recreate the sequence file.

        If that is not possible then you could modify the read ID's in some way to make them unique and then you should be able to use all the sequences (if this is a single end read dataset, with paired-end it would be difficult if both files are corrupt).

        Hopefully no other part of the file was corrupted by the event that messed up the ID's.

        Comment


        • #5
          Originally posted by Nino View Post
          No it is not a Sam file. A fastq file consists of a header from the machine it was sequence include genomic coordinates plus other information, second line consists of the read itself, third line which strand position, and lastly fourth line the base quality score. Have you ever looked into a fastq file before? Sam files hold much much more detailed information.
          See the fastq format description.



          The coordinates in the first line are not genomic coordinates, they are coordinates of the read on the flow cell, and include things like flow cell ID, lane number, tile number, and x,y coordinates.

          The third line has nothing to do with strand, it's always a +, optionally followed by the sequence identifier in the first line.

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          • #6
            Do you still have four lines for every read? Perhaps you could post a small section of the file so we can fully understand what you actually have.

            Comment

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