Any easy was to run a differential expression analysis?

Question

[williamsbrian5064]

I need some help with some RNA-seq data. All I want to do is a differential expression analysis but I'm struggling. Does anyone know of a simple up to date method to do this analysis? I tried using kallisto followed by Deseq2 but I can figure out how to get Deseq2 to work in R. I got Sleuth to work but I just have no idea how to interpret the data it gives me in their shiny app. Any help would be great.

[h.mon]

Have you read the Analyzing RNA-seq data with DESeq2 guide? It has complete instructions, from reading data to exploratory graphics and analysis to differential gene expression model set-up and analysis.

If you did read this guide, then tell us exactly where you are stuck at, with commands used, error messages and the output of sessionInfo().

Now, if you want something easier, search for differential expression shiny and you will be flooded by potentially very easy to use web apps.

[shoujun.gu]

You should follow DESeq/ DESeq2/edgeR vignette. If you cannot understand these documents, then it means it's beyond your ability to do the DE analysis. Go ahead and find some bioinformatician to help you.