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
> =========================================================
>
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>



-- 
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

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