4. Setting up terminal

If you decided to have your own computer

You can skip this section if you have core facility support. But read on if you don't and opt-out from having your own setup.

Using Galaxy

Before I talk about my own setup, you can totally skip setting up a terminal of yours if you have institutional backup or if you use Galaxy. If you are analyzing your own data, you can simply upload the fastq onto the Galaxy terminal. Or if you are fetching published data from GEO/SRA, you might want to try Faster Download and Extract Reads in FASTQ tool on Galaxy. It is essentially an one-stop-solution that it fetch and dump and fastq for you one click away. I will try to talk about this more in the relevant section, if I am going to make one.

Linux in Windows

You can also setup the pipeline on Windows 10 in the virtual Linux environment. It is super easy and you can get this done in half a day, skipping every single RNA-Seq tutorial on the Earth -

https://www.subioplatform.com/info_technical/349/how-to-setup-the-pipeline-of-the-rna-seq-fastq-file-processing-windows10-version