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--- mkatari-bioinformatics-august-2013-deseq [2013/08/23 15:53] – mkatari
+++ mkatari-bioinformatics-august-2013-deseq [2013/08/23 16:13] – mkatari
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 [[mkatari-bioinformatics-august-2013|Back to Manny's Bioinformatics Workshop HOME]]
-Here we will discuss how to create an R script (DESeq.R) that can be executed on HPC. Majority of the script is the same as if you were running it interactively except paths to the files are replaced with variables.
+Here we will discuss how to create an R script (DESeq.R) that can be executed on HPC. This script has been adapted from the DESeq manual [[ http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf|DESeq manual]]  except paths to the files are replaced with variables and the plots are being saved as pdf documents in an output directory.
 If you are going to run DESeq in R on your desktop you will have to make sure DESeq is already installed.
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-#DESeq manual: http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf