Alignment:
STAR --genomeDir genomes/Homo_sapiens_HG19_GRCh37_82 --sjdbGTFfile genomes/Homo_sapiens_HG19_GRCh37_82/Homo_sapiens_HG19_GRCh37_82.gtf --readFilesIn input/FILE01_R1.fastq input/FILE02_R2.fastq --runThreadN 10 --outSAMunmapped Within --outSAMstrandField intronMotif --outStd SAM | samtools view -bS - | samtools sort - outputdir/FILE1
 
Gene Counts:
featureCounts -T 10 -t exon -g gene_id -O -M -a genomes/Homo_sapiens_HG19_GRCh37_82/Homo_sapiens_HG19_GRCh37_82.gtf -o output/FILE1.geneCOUNT.txt output/FILE1.bam


Differential Gene Expression:
library("DESeq2")
Count_data<-read.table("Gene_counts.txt", header = T, quote = "", row.names = 1)
Count_data <- as.matrix(Count_data)
conditions=factor(c(rep("Ctrlsi_Prolif", 2), rep("Ctrlsi_IR", 2), rep("BAFFsi_IR", 2)))
coldata <- data.frame(row.names=colnames(Count_data), conditions)
dds <- DESeqDataSetFromMatrix(countData = Count_data, colData = coldata, design= ~conditions)
dds <- dds[rowSums(counts(dds)) > 0,]
dds <- DESeq(dds) 
res1 = results(dds, contrast=c("conditions","Ctrlsi_IR","Ctrlsi_Prolif"))
res2 = results(dds, contrast=c("conditions","BAFFsi_IR","Ctrlsi_IR"))


