Hi, I am trying to use "qrqc" package. I had two fastQ files (Illumina), one of which created about a year ago, and another was created a few months ago. The earlier one was read in using readSeqFile, and the latter one was not. I attach the error message from it with R version. The problem is about quality score format. I tried quality="phred" because for earlier one quality scores are Illumina Q score offset (ascii 64), and for latter one is in Sanger FASTQ format, the offset is ascii 33. I am wondering if I could change readSeqFile options to read the second fastQ file that is in Sanger FASTQ format created by Illumina. Thank you, SangChul Error messages. ========================================================= > fq.file <- readSeqFile("1.fq.gz") Error in readSeqFile("FASTQ019.fq.gz") : base quality out of range (0 <= b <= 62) encountered: 35 > fq.file <- readSeqFile("1.fq.gz",quality="phred") Error in readSeqFile("FASTQ019.fq.gz", : base quality out of range (4 <= b <= 60) encountered: 61 ========================================================= R version and sessionInfo. ========================================================= R Under development (unstable) (2012-02-14 r58341) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-apple-darwin10.8.0 (64-bit) other attached packages: [1] qrqc_1.3.0 ShortRead_1.13.12 latticeExtra_0.6-19 [4] RColorBrewer_1.0-5 Rsamtools_1.7.33 lattice_0.20-0 [7] Biostrings_2.23.6 GenomicRanges_1.7.24 IRanges_1.13.24 [10] BiocGenerics_0.1.4 =========================================================

Hi SangChul, As you mentioned, the Illumina Casava pipeline 1.8 now uses Sanger qualities. I have this change on Github, but Bioconductor does not have the most recent version (I will fix this though). For now, I recommend downloading the directory (using the download button, or you can clone the repo if you're familiar with Git) from here: https://github.com/vsbuffalo/qrqc Install as you would a source package or you can use "make build" and "make install" with the included Makefile. Hope this helps, Vince On Tue, Feb 14, 2012 at 3:00 PM, Sang Chul Choi <schoi@cornell.edu> wrote: > Hi, > > I am trying to use "qrqc" package. I had two fastQ files (Illumina), one > of which created about a year ago, and another was created a few months > ago. The earlier one was read in using readSeqFile, and the latter one was > not. I attach the error message from it with R version. The problem is > about quality score format. I tried quality="phred" because for earlier one > quality scores are Illumina Q score offset (ascii 64), and for latter one > is in Sanger FASTQ format, the offset is ascii 33. I am wondering if I > could change readSeqFile options to read the second fastQ file that is in > Sanger FASTQ format created by Illumina. > > Thank you, > > SangChul > > Error messages. > ========================================================= > > fq.file <- readSeqFile("1.fq.gz") > Error in readSeqFile("FASTQ019.fq.gz") : > base quality out of range (0 <= b <= 62) encountered: 35 > > > fq.file <- readSeqFile("1.fq.gz",quality="phred") > Error in readSeqFile("FASTQ019.fq.gz", : > base quality out of range (4 <= b <= 60) encountered: 61 > ========================================================= > > R version and sessionInfo. > ========================================================= > R Under development (unstable) (2012-02-14 r58341) > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > other attached packages: > [1] qrqc_1.3.0 ShortRead_1.13.12 latticeExtra_0.6-19 > [4] RColorBrewer_1.0-5 Rsamtools_1.7.33 lattice_0.20-0 > [7] Biostrings_2.23.6 GenomicRanges_1.7.24 IRanges_1.13.24 > [10] BiocGenerics_0.1.4 > ========================================================= > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Vince Buffalo Statistical Programmer Bioinformatics Core UC Davis Genome Center University of California, Davis "There's real poetry in the real world. Science is the poetry of reality." -Richard Dawkins [[alternative HTML version deleted]]