[BioC] how does ShortRead function identify score system

wang peter wng.peter at gmail.com
Thu Sep 20 04:57:15 CEST 2012

dear ALL:
       i have many RNA-seq data.
some use Phred+33 system to score the quality
some use Phred+63

i found no parameter to tell the functions which one should be.
but it still works
can you tell me which function can identify them.

such is the coding:
reads <- readFastq(fastqfile);

qual <- FastqQuality(quality(quality(reads)));
#qual <- PhredQuality(quality(quality(reads)));#

readM <- as(qual, "matrix");#注意R's maximum vector length is 2^31 - 1
pdf(file="boxplot.pdf"); # Save box plot as boxplot.pdf in current folder
boxplot(as.data.frame((readM)), outline = FALSE, main="Per Cycle Read
Quality", xlab="Cycle", ylab="Phred Quality");
# build per cycle boxplot

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

More information about the Bioconductor mailing list