Hello, I am new in DEseq2 analysis. I have tried to analyze my RNAseq data with GSEA software from Broad institute but didn't find anything satisfactory. I came across DEseq2 as most of the researchers use this approach. I will try to briefly explain my data that might help understand if there is any solution. I have collected the RNA from mouse embryonic retina of wild type and GTGF gene knock-out sample. Each type has three subtypes i.e. , WT1, WT2 WT3 and KO1, KO2 and KO3. The excel file contains the expression value to the genes (almost 17K genes). I want to see what pathways are altered globally. But I am clueless from where to start and how to start. I humbly ask to the community that if I can analyze all of the 17K genes or not.

Regards.

Have you worked through any DESeq2 tutorials?