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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. -
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
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
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