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To measure the frequency of indels at the ligation site you can use a vector with a unique restriction site in the lacZ gene. With a colorimetric assay you can count the number of white cfu. Perfect ligation in-frame yields blue cfu
The best resource for troubleshooting ligations I found (and use frequently) is this NEB page. That is assuming you've already referred to the instructions provided with the enzyme you're using. In my case it's T4 Ligase, again from NEB. It's helpful to check the FAQs and the references listed on that page. Also, you can make use of their Molar ...
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