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Pair-end mapping (PEM) is a technique that allows to detect structural variants in DNA by obtaining paired-end reads and the comparison of their positions in a reference genome. Then among libraries that had insertion of 500bp, 2kb, 10kb and 40kb which one would you pick to detect the following inversions?

a) an inversion mediated by inverted repeats of 20 kb at its breakpoints

b) an inversion with clean breakpoints (no inverted repeats)

c) an inversion mediated by inverted repeats of 1 kb at its breakpoints

My guesses:

a) 40kb, as if it were to be smaller than the inverted repeats length, the pair ends may align inside and nothing would be detected

b) Medium size, as if it is too small it wouldn't probably cover the area desired, and if it were bigger it would overlap too much (anyway data is needed for and answer is a blind optimization)

c) 2kb. same reasonings as a) and b).

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