On Sat, May 22, 2010 at 5:44 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 05/22/2010 03:38 PM, Peng Yu wrote: >> Hi Martin, >> >> '?FastqQuality' leads me to page with the first line 'QualityScore >> ? ? ? ? package:ShortRead ? ? ? ? ? ? R Documentation' >> >> Then I see, >> >> ? ? ?Use these functions to construct quality indicators for reads or >> ? ? ?alignments. See 'QualityScore' for details of object content and >> ? ? ?methods available for manipulating them. >> ... >> ? ? ?Constructors return objects of the corresponding class derived >> ? ? ?from 'QualityScore'. >> >> ... >> ? ? ?'QualityScore', 'readFastq', 'readAligned' >> >> >> However, when I query the helppage of QualityScore, I got nothing. >> >>> ?QualityScore >> No documentation for 'QualityScore' in specified packages and libraries: >> you could try '??QualityScore' > > ?"QualityScore-class" I don't see where the explanation of the difference between FastqQuality and SFastqQuality is. Is the first one for Sanger the second one for Illumina according to the following webpage? http://en.wikipedia.org/wiki/FASTQ_format There are totally 4 different Phred score scheme. Would you please let which correspond to which class in ShortRead package? S - Sanger Phred+33, raw reads typically (0, 40) X - Solexa Solexa+64, raw reads typically (-5, 40) I - Illumina 1.3+ Phred+64, raw reads typically (0, 40) J - Illumina 1.5+ Phred+64, raw reads typically (3, 40) with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) -- Regards, Peng

On 05/22/2010 06:39 PM, Peng Yu wrote: > On Sat, May 22, 2010 at 5:44 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> On 05/22/2010 03:38 PM, Peng Yu wrote: >>> Hi Martin, >>> >>> '?FastqQuality' leads me to page with the first line 'QualityScore >>> package:ShortRead R Documentation' >>> >>> Then I see, >>> >>> Use these functions to construct quality indicators for reads or >>> alignments. See 'QualityScore' for details of object content and >>> methods available for manipulating them. >>> ... >>> Constructors return objects of the corresponding class derived >>> from 'QualityScore'. >>> >>> ... >>> 'QualityScore', 'readFastq', 'readAligned' >>> >>> >>> However, when I query the helppage of QualityScore, I got nothing. >>> >>>> ?QualityScore >>> No documentation for 'QualityScore' in specified packages and libraries: >>> you could try '??QualityScore' >> >> ?"QualityScore-class" > > I don't see where the explanation of the difference between > FastqQuality and SFastqQuality is. Is the first one for Sanger the > second one for Illumina according to the following webpage? > > http://en.wikipedia.org/wiki/FASTQ_format > > There are totally 4 different Phred score scheme. Would you please let > which correspond to which class in ShortRead package? > > S - Sanger Phred+33, raw reads typically (0, 40) > X - Solexa Solexa+64, raw reads typically (-5, 40) > I - Illumina 1.3+ Phred+64, raw reads typically (0, 40) > J - Illumina 1.5+ Phred+64, raw reads typically (3, 40) with > 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) There are two different types of information here, quality score (phred vs. solexa) and encoding (+33 vs +64). FastqQuality is +33 encoding, SFastqQuality is +64 encoding. The classes are largely silent about the underlying interpretation of the score as phred versus solexa quality. Also ShortRead can arrive at the wrong representation, e.g., when reading a fastq file which contains quality scores but no indication of what scale those scores are read on or how they are encoded. Martin -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793