Copy the following in the opened R console, it should install all the packages under your own directory.
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicAlignments")
source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")If you encountered any problems, try to module load R before you open R console in the terminal.
srun -p class --pty bash #open a pseudo bash, -p: specify the partition
module load R #load the R module
R #open R console##### get raw read count on gene features
source("lib/readcount.R")
rc <- ReadCount(bamfile = "largedata/bamfiles.txt",
featureDB = "largedata/Osativa_204_v7.0.sqlite")bamfile: a txt file, each line indicates the location of your bam file.
featureDB: annotation database generated by GenomicFeatures
######## CBF and WT under nonstress
source("lib/DEG.R")
deg <- Run_DESeq2(rcdata=as.matrix(rc), colfile = "largedata/design.txt", designModel = formula(~ rep + tissue))rcdata: raw read count data generated from previous step.
colfile: for matrix input: a txt with at least a single column. Rows of colfile correspond to columns of countData. The design file must contains header. see below as an example. Note in columns fq1 and fq2, absolute or relative file locations should be specified.
fq1 fq2 rep tissue
leaf.rep1_1.fastq leaf/leaf.rep1_2.fastq rep1 leaf
leaf.rep2_1.fastq leaf/leaf.rep2_2.fastq rep2 leaf
leaf.rep3_1.fastq leaf/leaf.rep3_2.fastq rep3 leaf
root.rep1_1.fastq root/root.rep1_2.fastq rep1 root
root.rep2_1.fastq root/root.rep2_2.fastq rep2 root
root.rep3_1.fastq root/root.rep3_2.fastq rep3 rootdesignModel: A formula which specifies the design of the experiment, taking the form formula(~ rep + tissue). Note, the variables must match the header in colfile! By default, the functions in this package will use the last variable in the formula (e.g. tissue) for presenting results (fold changes, etc.) and plotting.