RNA sequence tutorial: the basics

This tutorial is perfect if:

• you are just starting bioinformatics and you want to learn how to install necessary softwares
• you want to replicate someone else's data in-house
• you are currently paying to convert fastq into read count files but you want to do it for free
• you have many samples to analyze and you want to do it fast & automatically

We will use Drosophila melanogaster as the model organism. The modules are in these sequences:

1. Basic installation guide

2. Learn how to convert 1 fastq into 1 read count file

3. Learn how to convert multiple fastq into 1 read count file

4. Learn how to conduct simple downstream analysis

Visit the Wiki page now to get started!

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Disclaimer

This tutorial was motivated by my own experience of struggling to build an RNA-seq pipeline, and is not intended to be the "correct" solution for everything; I used the combination of STAR align + featureCounts for the fast processing. My preferred coding language is Java, so if you find any mistakes in Python, R, or bash scripts I provided, please let me know!