Basic4Cseq, degenerate sites
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@theodoregeorgomanolis-7993
Last seen 18 months ago
Germany

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

Basic4Cseq basic4cseq degenerate sites • 484 views
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@carolin-walter-7897
Last seen 4.4 years ago
Germany

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

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@theodoregeorgomanolis-7993
Last seen 18 months ago
Germany

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

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