i tried to use ShortRead to get quality report but i am confused there is no parameter to set quality score type phred+33 or phred+64 library(ShortRead) fastqfile="P11_ACTTGA.fastq" qa <- qa(dirPath=".", pattern=fastqfile, type=c("fastq")) report(qa, dest="qcReport1", type="html") -- 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 Facebook:http://www.facebook.com/profile.php?id=100001986532253

On 08/14/2012 08:19 AM, wang peter wrote: > i tried to use ShortRead to get quality report > but i am confused there is no parameter to set quality score type > phred+33 or phred+64 > > library(ShortRead) > fastqfile="P11_ACTTGA.fastq" > > > qa <- qa(dirPath=".", pattern=fastqfile, type=c("fastq")) ShortRead supports only 'FastqQuality' and 'SFastqQuality'. Read the data as fq <- readFastq(".", fastqfile, qualityType="FastqQuality") qa(fq, fastqfile) for several files qas <- lapply(fls, function(fl) { fq <- readFastq(fl, qualityType="FastqQuality") qa(fq, basename(fl)) }) qa <- do.call(rbind, qas) > report(qa, dest="qcReport1", type="html") > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793