Question: alphabet/encoding IlluminaQuality SolexaQuality
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gravatar for felix.ernst
7 months ago by
felix.ernst0 wrote:

Hi,

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.

Felix

 

biostrings xstringquality • 159 views
ADD COMMENTlink written 7 months ago by felix.ernst0
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