RNASeq

>wget http://sourceforge.net/projects/useq/files/USeq_6.7.zip/download
>unzip USeq_6.7.zip
>java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) 64-Bit Server VM (build 16.3-b01, mixed mode)

>java -jar RNASeq
**************************************************************************************
** RNASeq: June 2010 **
**************************************************************************************
Example: java -Xmx2G -jar pathTo/USeq/Apps/RNASeq -y eland -v D_rerio_Dec_2008 -t
/Data/PolIIRep1/,/Data/PolIIRep2/ -c /Data/PolIINRep1/,/Data/PolIINRep2/ -s
/Data/Results/WtVsNull -g /Anno/zv8Genes.ucsc

**************************************************************************

>apt-get install r-base-core
>R

R>source("http://www.bioconductor.org/biocLite.R")

R>biocLite("DESeq")

>R CMD INSTALL DESeq_1.1.8.tar.gz



Install Galaxy on Bioserver(bioserver.hci.utah.edu)

#Install R
>wget http://cran.cnr.berkeley.edu/src/base/R-2/R-2.11.1.tar.gz
>tar zxvf R-2.11.1.tar.gz
>configure && make && make install

#Put R into environment


#Start R
>R
>source('http://www.bioconductor.org/biocLite.R')
>biocLite('DESeq')



java -Xmx2G -jar pathTo/USeq/Apps/RNASeq -y eland -v D_rerio_Dec_2008 -t
/Data/PolIIRep1/,/Data/PolIIRep2/ -c /Data/PolIINRep1/,/Data/PolIINRep2/ -s
/Data/Results/WtVsNull -g /Anno/zv8Genes.ucsc


galaxy@bioserver>java -Xmx2G -jar /home/galaxy/tools/USeq_6.7/Apps/RNASeq -y eland -v D_rerio_Dec_2008 -c /home/galaxy/tmp/OverDispersedRNASeqDataset/Novoalignments/Control -t /home/galaxy/tmp/OverDispersedRNASeqDataset/Novoalignments/Treatment -g /home/galaxy/tmp/OverDispersedRNASeqDataset/hg19EnsGenes.ucsc -s /home/galaxy/tmp/hello -r /home/galaxy/tools/R-2.11.1/bin/R


time java -Xmx2G -jar /home/ying/tools/USeq_6.7/Apps/RNASeq -y eland -v D_rerio_Dec_2008 -c /home/ying/tmp/OverDispersedRNASeqDataset/Novoalignments/Control -t /home/ying/tmp/OverDispersedRNASeqDataset/Novoalignments/Treatment -g /home/ying/tmp/OverDispersedRNASeqDataset/hg19EnsGenes.ucsc -s /home/ying/tmp/hello