Is there a way to extend the analysis for the degenerate restriction sites like ApoI?

the createVirtualFragmentLibrary function does not work when I enter restriction sites such as RAATTY (ApoI)

Thank you for your answer

Hi,

I'm sorry, but Basic4Cseq doesn't support degenerate sites. I tried a simple approach for this problem months ago, and it caused more trouble than it was worth. Since I can't promise to solve this issue in the near future, I'd suggest using another algorithm for your data.

Best,

Carolin

Thank you for your answer.
Then, what about a way to inject custom bed generated file of the restriction sites into the Basic4Cseq list?
To be honest I am intrigue by your implementation of the statistics based on the:

Stadhouders. et al., 2012, van de Werken et al., 2012. Splinter et al., 2012.
I can deduce most of them "manualy" but it would be nice to have an R script (R is not my thing!!!).

Anyway, I will also try some other implementations

Theo