        library(ShortRead);
        reads <- readFastq(fastqfile);
        seqs <- sread(reads);
 qual <- quality(quality(reads));

   score_sys = data.class(quality(reads));#
   cat("the quality score system
(SFastqQuality=Phred+64,FastqQuality=Phred+33) is",score_sys,"\n")

it is a Phred+64 system, how can i change the qual to Phred+33. then i can
make new reads by
reads <- ShortReadQ(sread=seqs, quality=qual, id= BStringSet(paste0(sample,
"-", first_number:last_number) ) );

-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute for Plant Research
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839@cornell.edu
Facebook:http://www.facebook.com/profile.php?id=100001986532253

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