[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.
> 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
Platform: x86_64-apple-darwin10.8.0 (64-bit)
other attached packages:
 qrqc_1.3.0 ShortRead_1.13.12 latticeExtra_0.6-19
 RColorBrewer_1.0-5 Rsamtools_1.7.33 lattice_0.20-0
 Biostrings_2.23.6 GenomicRanges_1.7.24 IRanges_1.13.24
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