From eca8bb0bdf0b094f8917f56fcf66cd33615be60b Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Fri, 10 Dec 2010 13:33:38 +0000
Subject: [PATCH] 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
---
.../source/bash/CreatePerCycleReadQuality.R | 11 -----------
1 file changed, 11 deletions(-)
delete mode 100644 deep_sequencing_unit/source/bash/CreatePerCycleReadQuality.R
diff --git a/deep_sequencing_unit/source/bash/CreatePerCycleReadQuality.R b/deep_sequencing_unit/source/bash/CreatePerCycleReadQuality.R
deleted file mode 100644
index 3baeb2ba76e..00000000000
--- a/deep_sequencing_unit/source/bash/CreatePerCycleReadQuality.R
+++ /dev/null
@@ -1,11 +0,0 @@
-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()
\ No newline at end of file
--
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