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Exclusions taking into account PAM cutting #37

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batson opened this issue Dec 1, 2018 · 0 comments
Open

Exclusions taking into account PAM cutting #37

batson opened this issue Dec 1, 2018 · 0 comments

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@batson
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batson commented Dec 1, 2018

If one guide cuts in the middle of another's PAM site, no confetti is generated.

Thus sufficiently nearby guides need not be excluded, which may help with the problem of densely mutated genomes.

This can be added for free in the constraint setting, depending on if guides are forward or backwards, looking for cut site of one inside the other's window or vv. In particular, if A --> !B, then we can have A and B in the set (hoping that sometimes A will cut first). Thus we check if either would exclude the other. This can mean that guides right next to one another (in a 22bp window) are fine, though we should make sure not to count them for credit in the optimizer (ie, only one of the neighboring cuts counts for credit). That statement may be slightly trickier if there are cascades, not just pairs.

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