the coding can works well on many data.
but when it works on 12 lines, i met such a problem

how can the function tell the score if 33 or 64 system?

library(ShortRead);
reads <- readFastq(fastqfile);
seqs <- sread(reads);
score_sys = data.class(quality(reads));
cat("the quality score system
(SFastqQuality=Phred+64,FastqQuality=Phred+33) is",score_sys,"\n")


the output is:
the quality score system (SFastqQuality=Phred+64,FastqQuality=Phred+33) is
SFastqQuality
but it is really the FastqQuality=Phred+33

@HISEQ04:126:C343UACXX:8:1103:15851:74641 1:N:0:ACAGTG
GGCCTCTCAATGTCAAGGGATCGACGGCAGATATCATAGATGGCCTCATTGTCCAAGAGAACTGCGACATCTGTGTGCTCGAGCAAGGAATGAGTGGAAAG
+
BBBFFFFFFFFFFFFIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFBFFFFBFFFFFFFFFFFFFFFFFFFFFFBFFFBFB
@HISEQ04:126:C343UACXX:8:1103:16187:74529 1:N:0:ACAGTG
CAATTCTAGCTACTGGAGCTGTCCATTTGCCGCGCAGGCACTGAAGATAGAACATCGATCGAGTCAACCTCTACCTGCATTAGGTGACTGCTGAGAGCTCC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFBFFFFFFFFFFFFFBFFFFFFBFFFFFFFFFFFFFFFF
@HISEQ04:126:C343UACXX:8:1103:16244:74553 1:N:0:ACAGTG
GCCGAAGCATTTTTGGCTTCTGTAAGGTTGTACATATGAAGCAGATTGCTCCAGCTTGGAAGAGTCATGTTTGTGACGAGAGAACTGGCTACAGCTCCAGG
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIFFIFIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIFFFIIFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFF


-- 
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]]

