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Reference Genome/FastQ directionality standards

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  • Reference Genome/FastQ directionality standards


    Is the Reference Genome hg19/GRCh37 represented in 5' -> 3' direction or 3' -> 5' direction?

    In general are FastQ/FQ/Fasta/FA files 5'->3' or 3'->5' ?

    For FastQ files representing a coding region is showing the sense strand the standard?

    I apologize for the extremely basic question, but I try as I might, I can't seem to find a solid answer as there doesn't appear to be a standardization scheme for the the FASTQ format type.

    Thank you,

  • #2
    DNA sequences are always reported in the 5' -> 3' direction, unless it is explicitly stated otherwise. Regardless of the file format, FASTA, FASTQ, Gebank, etc., and without any information to the contrary, it is safe to assume the DNA as written is 5' -> 3'.


    • #3
      Thanks for your quick reply, it's good to know I've been working under the correct assumption.


      • #4
        Well, if you get a FASTQ file from a sequencing machine, that machine doesn't know anything about what strand is usually transcribed in cells, or if it's a coding region at all. It just reads whatever fragments of DNA are floating around. So you will get reads from both strands.


        • #5
          yeah, you get reads from both directions, and only way to know is align to a reference and see which strand it matches... except some directionally aware rna-seq where all sequence reads are just a single strand