Question: DESeq2 - Comparing RNA-Seq and Ribo-Seq
gravatar for timjoncooper
6 days ago by
timjoncooper0 wrote:

I'm attempting to compare total RNA-seq with Ribo-Seq, to determine if changes in Ribo-Seq are due to changes in transcriptional expression (akin to the analysis performed by Anota2Seq). I am, however, struggling to understand how to accomplish this in DESeq2.

My design is as follows:

cts <- read.delim("Interaction.txt", row.names=1)
coldata <- read.delim("Sample_Sheet.txt", row.names=1)
cts <- round(cts)
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~Genotype + Type + Genotype:Type)
dds <- DESeq(dds)

> coldata
                Genotype Type
C_24h_Ribo_1     Control Ribo
C_24h_Ribo_2     Control Ribo
C_24h_Ribo_3     Control Ribo
CHIK_24h_Ribo_1    Viral Ribo
CHIK_24h_Ribo_2    Viral Ribo
CHIK_24h_Ribo_3    Viral Ribo
C_24h_RNA_1      Control  RNA
C_24h_RNA_2      Control  RNA
C_24h_RNA_3      Control  RNA
CHIK_24h_RNA_1     Viral  RNA
CHIK_24h_RNA_2     Viral  RNA
CHIK_24h_RNA_3     Viral  RNA

> resultsNames(dds)
[1] "Intercept"                 "Genotype_Viral_vs_Control" "Type_RNA_vs_Ribo"          "GenotypeViral.TypeRNA"

I do not understand which contrast is the one I need, or how to access the results i'm looking for (or interpret them). Any help?

deseq2 • 55 views
ADD COMMENTlink modified 5 days ago by Michael Love24k • written 6 days ago by timjoncooper0
Answer: DESeq2 - Comparing RNA-Seq and Ribo-Seq
gravatar for Michael Love
5 days ago by
Michael Love24k
United States
Michael Love24k wrote:

Take a look at the vignette section on interactions which includes a diagram. GenotypeViral.TypeRNA is an interaction term here.

ADD COMMENTlink written 5 days ago by Michael Love24k
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