On 01/11/2012 01:05 PM, wang peter wrote: > dear martin? > the Illumina1.3+(Phred+64) is not Solexa score, > > YOU CAN SEE : > > > Score Offset phred ASCII > > Sanger 33 0?93 33?126 > Solexa 64 -5?62 59?126 > Illumina1.3+ 64 0?62 64?126 > > > if i use solexa function to deal with Illumina1.3+, is it compatible? In ShortRead, FastqQuality and SFastqQuality determine the _encoding_; SFastqQuality is appropriate for Solexa and Illumina1.3+. Functions in ShortRead, e.g., alphabetScore() or as(quality(), "matrix") operate on the integer value of the corresponding letter. ShortRead does not (unless I am missing some code) translate the encoding into probabilities. Biostrings PhredQuality and SolexaQuality also represent encoding, but allow coercion to numeric, as(<...>, "numeric"). These coercions use -10 log10 (p) for PhredQuality, -10 log10(p / 1-p) for SolexaQuality. The latter is not appropriate for Illumina1.3+ (although the differences are most pronounced when p is large, i.e., when reads have low quality anyway). I will add an additional class IlluminaQuality, to Biostrings in the 'devel' branch. Martin -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793