Kit manuals include tables that describe the adaptor and primer oligos. Most of the symbols seen here conform to IUPAC standards whereas others seem to be arbitrary symbols. I am interested in any resources that document the modifications which pertain to bioinformatic analysis. In this case, I am trying to determine the sequences I should include in my cutadapt script for trimming. The manual from which I cut the image below assumes knowledge of all symbols except for * which they designate as a phosphorothioate bond. I think I have an idea about the remaining symbols, but I can't find confirmation for all of them. Hopefully this community can provide more insight.
symbols and best guess:
[ rApp ] - Adenosine with diphosphate backbone? Would this base be sequenced or somehow ejected during library prep?
[ rG ] - Guanosine
[ rU ] - Uridine
[ rC ] - Cytidine
[ NH2 ] - primary amine
If I'm correct about the rN set representing ribonucleotides, it would be appropriate to replace there with standard A T C G notation for adaptor oligo input to cutadapt. What is the function of the rApp in the 3' Adaptor? Are there other oligo modifications that are relatively common and require special treatment in bioinformatics analyses?