Basic4Cseq, degenerate sites
2
0
Entering edit mode
Theo ▴ 10
@theodoregeorgomanolis-7993
Last seen 4 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 • 1.1k views
ADD COMMENT
0
Entering edit mode
@carolin-walter-7897
Last seen 7.4 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

ADD COMMENT
0
Entering edit mode
Theo ▴ 10
@theodoregeorgomanolis-7993
Last seen 4 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

ADD COMMENT

Login before adding your answer.

Traffic: 754 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6