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  • Question in terminology

    Dear all,

    I received a file with some explenation about a sequence, however there is something I dont understand.


    "A K-mer refers to an artificial sequence division of K nucleotides. A raw sequencing read with L bp contains (L-K+1) K-mers if the length of each K-mer is K bp. The frequency of each K-mer can be calculated from the raw genome sequencing reads"

    I know what a K-mer is, but where do they get the L bp from?
    What is this L bp?


  • #2
    Length in bases Id guess.. Makes sense

    Comment


    • #3
      Originally posted by JackieBadger View Post
      Length in bases Id guess.. Makes sense
      Yes I know its a length of bases, but what does it represent?

      What is the L bp in relationship to the K-mer?

      Is the K-mer a piece of the L bp ?

      Comment


      • #4
        Question in terminology

        L is the length of the read in base pairs, and yes, the k-mer is a piece of the read.

        For example, if you had a read that was 50 bp long, and wanted to use k-mers of length 47, then you would get 50-47+1=4 kmers from your read.

        The first kmer would be bases 1-47 of the read, the second kmer would be bases 2-48 of the read, the third kmer bases 3-49 and the fourth one bases 4-50, assuming you were also using a step size of 1.

        Are you doing de novo assembly?

        Comment


        • #5
          Originally posted by mastal View Post
          L is the length of the read in base pairs, and yes, the k-mer is a piece of the read.

          For example, if you had a read that was 50 bp long, and wanted to use k-mers of length 47, then you would get 50-47+1=4 kmers from your read.

          The first kmer would be bases 1-47 of the read, the second kmer would be bases 2-48 of the read, the third kmer bases 3-49 and the fourth one bases 4-50, assuming you were also using a step size of 1.

          Are you doing de novo assembly?
          Ah ok.
          It also said: Typically, K = 17.
          So I guess they use 17 as a stanard length.

          I am not doing it myself, we are doing it with the help of a company that does it for us.

          But indeed, the goal is a de novo assembly.

          Comment


          • #6
            17 is an arbitrary size. Depending on the assembler, the length of the reads, and their quality, quite frequently much higher values will give you better assembles.

            Note that most assemblers prefer/demand odd length kmers, so that no kmer is its own reverse complement. Programs using kmers for other purposes may not impose that restriction.

            Comment


            • #7
              Originally posted by krobison View Post
              17 is an arbitrary size. Depending on the assembler, the length of the reads, and their quality, quite frequently much higher values will give you better assembles.

              Note that most assemblers prefer/demand odd length kmers, so that no kmer is its own reverse complement. Programs using kmers for other purposes may not impose that restriction.
              Ok, I see what you mean.
              I allready had that idea.
              The odd numbered lenght kmers sounds logical! Good you told me, I would not have figured that out myself I think.

              Comment


              • #8
                Originally posted by krobison View Post
                Note that most assemblers prefer/demand odd length kmers, so that no kmer is its own reverse complement. Programs using kmers for other purposes may not impose that restriction.
                Could you explain this?
                I do not see why it has to be an odd number.
                Perhaps with a simple example.

                Comment


                • #9
                  AAATTT: reverse complement is the same.
                  AAAATTT: reverse complement is AAATTTT.

                  Comment

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