i read the fastq file and let the function identify the quality score if(iteration==1)# { score_sys = data.class(quality(reads)); } if(score_sys =="SFastqQuality")#Phred+64 { do something } if(score_sys =="FastqQuality")#Phred+33 { do something } but the score_sys=SFastqQuality, the data is Phred+33 see the quality line HHHHHHHHHHHHHHHHHHGHHHHHHDDCDD#?CCBCDDDCHEHHHHHHHHHHHFH7 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

Hi -- If I make a plain text file 'test.fq' with just these four lines in it > id AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA @ id HHHHHHHHHHHHHHHHHHGHHHHHHDDCDD#?CCBCDDDCHEHHHHHHHHHHHFH7 and then read it in I get FastqQuality > data.class(quality(readFastq("/tmp/tmp.fq"))) [1] "FastqQuality" Do you? The algorithm uses a heuristic and looks at the first 1000 reads alf <- alphabetFrequency(head(quality, 1000), collapse = TRUE) if (any(alf) && min(which(alf != 0)) < 59) { FastqQuality } else SFastqQuality so if you have high-quality reads initially it will guess wrong; I'll increase the number of reads looked at. Martin On 11/29/2012 07:48 PM, Wang Peter wrote: > i read the fastq file and let the function identify the quality score > > if(iteration==1)# > { > score_sys = data.class(quality(reads)); > } > if(score_sys =="SFastqQuality")#Phred+64 > { > do something > } > if(score_sys =="FastqQuality")#Phred+33 > { > do something > } > > > but the score_sys=SFastqQuality, the data is Phred+33 > > see the quality line > HHHHHHHHHHHHHHHHHHGHHHHHHDDCDD#?CCBCDDDCHEHHHHHHHHHHHFH7 > -- 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