I am bit new to using XStringQuality information. However I noticed, that encoding() and alphabet() return NA values for values not included in the Illumina/Solexa scores.
The manual says values between 0:99/-5:99 are accepted. How should this be interpreted? Do the classes follow current encodings or maybe older ones? (I did find conflicting information for Illumina scores and the current encodings are a subset of the ones reported by alphabet/encoding)
It boils down to this question: Do I need to/should do sanity checks, if I import sequences from fastq files?
Thanks for any advice and help.