[BioC] how to plot quality report

[Martin Morgan]

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")
>


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