i remember the shortread package can identify the read score system is phred+33 or 64 if i use reads <- yield(inFh) or reads <- readFastq(fastqfile);\ how can i get that information from the reads? thank you -- 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

On 11/8/2012 4:18 PM, wang peter wrote: > i remember the shortread package can identify the read score system is > phred+33 or 64 > > if i use > > reads <- yield(inFh) > or reads <- readFastq(fastqfile);\ > > how can i get that information from the reads? quality(reads) returns an object that displays either class: SFastqQuality in which case the reads are 'Solexa' (phred + 64) encoded or class: FastqQuality in which case they are phred + 33 encoded. ?readFastq contains information on this. Martin > > thank you > -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109