moved to R dir

This line, and those below, will be ignored--
D    svn+ssh://svncisd@svncisd.ethz.ch/repos/cisd/deep_sequencing_unit/trunk/source/bash/CreatePerCycleReadQuality.R

SVN: 19088

deep_sequencing_unit/source/bash/CreatePerCycleReadQuality.R

-library(ShortRead)
-args <- commandArgs(TRUE)
-reads <- readFastq(args[1])
-if (length(reads) > 1000000) {
-	reads <- sample(reads,1000000) # if more than a million reads, sample randomly
-}
-qual <- FastqQuality(quality(quality(reads))) # get quality scores
-readM <- as(qual, "matrix") # convert scores to matrix
-pdf(file=paste(args[1],"boxplot.pdf", sep="_")) # Save box plot as boxplot.pdf in current folder
-boxplot(readM, outline = FALSE, main="Per Cycle Read Quality", sub=args[1], xlab="Cycle", ylab="Phred Quality", col="grey")
-dev.off()
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