[BioC] Error in readSeqFile of qrqc package?

Sang Chul Choi schoi at cornell.edu
Wed Feb 15 00:00:46 CET 2012


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,


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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