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 [[alternative HTML version deleted]]