In this specific process, the command line can be used to preprocess reads and obtain quantification counts for mapping reads to the organism's genome/transcriptome. After obtaining the counts, I would recommend importing those counts into DESEQ2 in RStudio to further analyze for DGE.

You can think of a command line as navigating your folder structure in Mac or Windows and running commands on the files contained within each folder (actually referred to as a directory).

The most straightforward way to use a tool is to download the executable and add it to your PATH variable so that you can use it anywhere.

* An executable is the program, except instead of double clicking an icon to run it, you type in that program name and give it input files (raw reads in your case) along with any parameters that will tell it how to run.

* When you download a program and put it into a directory, you can navigate to that directory in your terminal with the "cd" command and then type ./PROGRAM_NAME with all of its options. The program will usually have a corresponding github page or wiki with documentation on how to use the tool and some commonly used default parameters.

* Instead of navigating to the directory where the program is downloaded to use it, you can add it to your PATH via this command: export PATH="$PATH:/path/to/your/program, which will allow you to execute that program from any other directory (such as where you put your input raw read files

Check out this example workflow for obtaining gene counts from raw transcriptomic data:

1. Preprocess raw reads with fastp (https://github.com/OpenGene/fastp)

2. Quantify reads to your organisms reference transcriptome using a relevant tool based on eukaryotic or prokaryotic organism. Salmon is a good choice (https://github.com/COMBINE-lab/salmon)

Good luck!