RNAseq 1 control 2 different treatment

Question

[matteo.levorato]

Hello,

I am analyzing RNAseq data coming from an experiment that concerns 2 different and independent treatment. I am wondering how should I perform RNAseq analysis to obtain DEGs from each condition and on top of that the DEGs shared between the two treatment and the exclusive ones. Which kind of approach should I use?

Especially, I would like have a for cycle that for each gene present in the result dataframe of condition 1 check if the same gene in the result dataframe of the condition 2 has a log2FoldChange between -0.1 and 0.1, and save it in a new dataframe.

Thank you so much in advance

[sansan96]

I think what you should do is do differential expression for your two contrasts: treatment 1 vs control and treatment 2 vs control. DESeq2 has a function for contrast:

Treatment1_vs_Control <- results(dds, contrast = c("condition", "treatment1", "control"))
Treatment2_vs_Control <- results(dds, contrast = c("condition", "treatment2", "control"))

After that, you can find the exclusive and shared genes of each contrast through Venn or Upset plot. Here are some tools:

https://bioinformatics.psb.ugent.be/webtools/Venn/

https://csbg.cnb.csic.es/BioinfoGP/venny.html

[matteo.levorato]

yes, this is what I did. However, since my treatments are very similar each other, when I check upregulated genes in one treatment, they are also upregulated in the other one. It is for this reason that I would like to implement the 'for' cycle mentioned above, but I am not really able to make it my self.