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  • repeats

    I am trying to find a repeat regions (not Transposons). Is there a way i can find a 50 bp region repeating across the genome ?. Need to find the number of times that 50 bp is repeating in the genome.
    I have tried GEM-mappability and Uniqueome, but GEM-mappability didnt work. Current version of GEM-tools do not have this feature. Uniqueome gives a score and it depends on the sequencing data. But i dont have any sequence data.
    -Alaguraj.V

  • #2
    One approach would be to take the frequency of all 50-mers across the genome (those not matching TEs), and you could then map those to the genome to identify the location/depth of the repeats. Both steps could be accomplished with Vmatch or Tallymer.

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