Forum:Learning RNASeq Analysis using my own DATA that needs to be analyzed

Question

[Nattoh Godfrey]

I recently did RNASeq and have the Paired-end read, I have checked quality in FastQC and trimmed the ends with Trimmomatic. Does any one have a pipeline I could use to do downstream analysis. I have been learning online/youtube etc. No formal training on these kind of analysis. I am interested in differential expression profiles (compare Control and Treatment), and identify unique genes expressed at different stages on my treatment.

[cpad0112]

Try reproducing griffith lab tutorial on RNAseq (https://github.com/griffithlab/rnaseq_tutorial)

Answer 1

[Kristoffer Vitting-Seerup]

For an overview the different ways to analyze your data you can refere to this.

With regards to gene DE analysis there are two major ways you can go:

Option 1) I just want to get this done asap. There are many possibilities but you can use a tool like 3D RNA-seq or Galaxy

Option 2) I want to learn some bioinformatics and R coding along the way: Again there are many options but a good place to start is this workflow using DESeq2 which have links to the other things you need.