While reviewing the source code of your CRISPRseek package I am confused about one thing. While examining the buildFeatureVectorForScoring function, I saw that it was written differently in the source code I downloaded and the R program. I'm confused as to which one is the latest version. I would be very grateful if you could explain why this difference. In BuildFeatureVectorForScoring2 function, the r.nucleotide [r.nucleotide == "T"] = "U" line failed when r.nucleotide contained "T". I think the reason is that the variable r.nucleotide in the previous line is perceived as a DNA sequence since it was created with DNAStringSet, and therefore does not contain "Uracil".

Hi Sezer Islambey,

Thanks for the question! That line of code is used to convert all Ts to Us which is required by the downstream analysis, which assumes U instead of T. FYI, this is an internal function and not meant to be called directly.

Best,

Julie