by the way
* Quality assessment
Use ShortRead to produce a basic QA report. Down-sample fastq files if
they are big.
 library(ShortRead)
 fls <- list.files(fastqDir, "fastq$", full=TRUE)
 names(fls) <- sub(".fastq", "", basename(fls))
 ## use FastqSampler if fastq files are large
 qas <- lapply(seq_along(fls),
               function(i, fls) qa(readFastq(fls[i]), names(fls)[i]),
               fls)
 qa <- do.call(rbind, qas)
 save(qa, file=file.path(outputDir, "qa.rda")
 browseURL(report(qa))

in the line of qas, i means the ith file. do u need write a loop to assign i
thx
shan gao

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