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Commit 0022645d authored by Bhanu Priya's avatar Bhanu Priya
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Add pipeline 2 - DGE analysis

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1 merge request!1Add pipeline 2 - DGE analysis
Sample Condition
SRR15322680 Metastatic
SRR15322681 Metastatic
SRR15322682 Metastatic
SRR15322683 Primary
SRR15322684 Primary
SRR15322685 Primary
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/080/SRR15322680/SRR15322680_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/080/SRR15322680/SRR15322680_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/081/SRR15322681/SRR15322681_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/081/SRR15322681/SRR15322681_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/082/SRR15322682/SRR15322682_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/082/SRR15322682/SRR15322682_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/083/SRR15322683/SRR15322683_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/083/SRR15322683/SRR15322683_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/084/SRR15322684/SRR15322684_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/084/SRR15322684/SRR15322684_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/085/SRR15322685/SRR15322685_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR153/085/SRR15322685/SRR15322685_2.fastq.gz
#!/usr/bin/env Rscript
library(edgeR)
RawCounts <- read.delim("count_matrix.txt", row.names = "gene_id")
group <- read.table("SampleGroups.txt", header=TRUE, sep="\t", row.names=1)
dgecomplete <- DGEList(RawCounts, group = group$Condition)
logcpm <- cpm(dgecomplete, log=TRUE)
filtData <- filterByExpr(dgecomplete)
dgecomplete <- dgecomplete[filtData, keep.lib.sizes=FALSE]
dgecomplete <- calcNormFactors(dgecomplete)
dgecomplete <- estimateDisp(y = dgecomplete)
fit <- glmQLFit(y=dgecomplete)
qlf <- glmQLFTest(fit, coef = 2)
diff_results <- topTags(qlf, n=Inf)
write.csv(diff_results, file="edgeR_diff_genes.csv")
write.csv(as.data.frame(logcpm), file="edgeR_normcounts.csv")
#!/usr/bin/env bash
FILES=$(cat ./data/SampleInputFileLinks.txt)
for file in $FILES; do
# --no-clobber, do not download if file already exists.
wget -nc $file
done
hisat2-build -p 8 genome.fa hg38_hisat
hisat2 –x index -1 sample1_trim_R1.fq -2 sample1_trim_R2.fq –U unpair.fq –S sample1.sam
htseq-count –r sample1.sam sample2.sam samplen.sam hs.gff > count_matrix.txt
Rscript dge_analysis.r
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